Variant report

Variant	rs2106109
Chromosome Location	chr22:23499674-23499675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:23499317..23501523-chr22:23519900..23522809,2	MCF-7	breast:
2	chr22:23487286..23490027-chr22:23497824..23500651,3	MCF-7	breast:
3	chr22:23499285..23501441-chr22:23509094..23511790,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186716	Chromatin interaction
ENSG00000236794	Chromatin interaction
ENSG00000100228	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10775764	0.90[ASN][1000 genomes]
rs12484280	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1807702	0.88[ASN][1000 genomes]
rs1807705	0.88[ASN][1000 genomes]
rs1807706	0.90[ASN][1000 genomes]
rs1987043	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2008176	0.90[ASN][1000 genomes]
rs2071431	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2071432	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2071433	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2071434	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2071435	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2071436	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2246716	0.86[ASN][1000 genomes]
rs2249692	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2267007	0.90[ASN][1000 genomes]
rs2267008	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2267009	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2267011	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2283802	0.82[AMR][1000 genomes]
rs2301554	0.80[ASN][1000 genomes]
rs2301555	0.85[ASN][1000 genomes]
rs2330361	0.86[ASN][1000 genomes]
rs3761418	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3788356	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3788357	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4552283	0.90[ASN][1000 genomes]
rs4820538	0.82[AMR][1000 genomes]
rs4820541	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4820542	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4822369	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55637879	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5751590	0.82[ASN][1000 genomes]
rs5751593	0.90[ASN][1000 genomes]
rs5751596	0.91[ASN][1000 genomes]
rs5751597	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5751598	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5751600	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5751601	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5751602	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5751603	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5751606	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5751607	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5759604	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5759607	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5759608	0.90[ASN][1000 genomes]
rs5759609	0.90[ASN][1000 genomes]
rs5759611	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5759612	0.89[ASN][1000 genomes]
rs5759613	0.90[ASN][1000 genomes]
rs5759614	0.90[ASN][1000 genomes]
rs5759615	0.90[ASN][1000 genomes]
rs5759616	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5759617	0.89[ASN][1000 genomes]
rs5759618	0.90[ASN][1000 genomes]
rs5759619	0.88[ASN][1000 genomes]
rs5759620	0.90[ASN][1000 genomes]
rs5759621	0.90[ASN][1000 genomes]
rs5759622	0.88[ASN][1000 genomes]
rs5759624	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5759628	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5759629	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5759630	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5759631	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5759635	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5759637	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5759638	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57983679	0.85[ASN][1000 genomes]
rs5996483	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60037456	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6519421	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs713617	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs713682	0.90[ASN][1000 genomes]
rs7289172	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73152631	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs737818	0.90[ASN][1000 genomes]
rs737819	0.88[ASN][1000 genomes]
rs737820	0.90[ASN][1000 genomes]
rs756633	0.90[ASN][1000 genomes]
rs768514	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8138361	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8142746	0.90[ASN][1000 genomes]
rs9608085	0.90[ASN][1000 genomes]
rs9612244	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9612251	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9612252	0.90[ASN][1000 genomes]
rs9612253	0.90[ASN][1000 genomes]
rs9624047	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9624048	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9624049	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9624050	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9624051	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915235	chr22:22971768-23650987	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
2	esv3388845	chr22:22973346-23652447	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	100 gene(s)	inside rSNPs	diseases
3	nsv531799	chr22:22993679-23642142	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
4	nsv1061433	chr22:22997799-23649107	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
5	nsv521695	chr22:22998337-23648009	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
6	nsv915236	chr22:22998337-23650987	Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
7	nsv588512	chr22:22998337-23667731	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
8	nsv531800	chr22:23002708-23648163	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
9	nsv916593	chr22:23002709-23648790	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
10	nsv993496	chr22:23002709-23654222	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
11	nsv1067002	chr22:23007167-23643363	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
12	nsv1067324	chr22:23007367-23654223	Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
13	nsv533839	chr22:23012013-23643223	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
14	nsv916933	chr22:23012069-23654237	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
15	nsv531801	chr22:23028586-23657804	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	92 gene(s)	inside rSNPs	diseases
16	nsv531802	chr22:23046186-23627391	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	diseases
17	nsv1060509	chr22:23055148-23648719	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	83 gene(s)	inside rSNPs	diseases
18	nsv1056324	chr22:23055148-23750989	Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
19	nsv1062780	chr22:23060449-23648719	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
20	nsv948942	chr22:23063178-23645718	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
21	nsv1063200	chr22:23097177-23643224	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	80 gene(s)	inside rSNPs	diseases
22	nsv949250	chr22:23157485-23645718	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
23	nsv1057659	chr22:23400739-24138788	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
24	nsv1058604	chr22:23497533-23545751	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2106109	BCR	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:23488200-23505800	Weak transcription	HSMMtube	muscle
2	chr22:23488400-23505800	Weak transcription	Brain Substantia Nigra	brain
3	chr22:23488600-23505800	Weak transcription	Brain Germinal Matrix	brain
4	chr22:23488600-23506800	Weak transcription	A549	lung
5	chr22:23488800-23505400	Weak transcription	Fetal Brain Male	brain
6	chr22:23489200-23499800	Weak transcription	NHLF	lung
7	chr22:23490200-23500200	Weak transcription	Fetal Lung	lung
8	chr22:23490200-23504800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr22:23490400-23506800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr22:23490400-23522000	Weak transcription	Aorta	Aorta
11	chr22:23491000-23504600	Strong transcription	Stomach Smooth Muscle	stomach
12	chr22:23491200-23512000	Strong transcription	Right Atrium	heart
13	chr22:23492200-23505800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr22:23492400-23509000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr22:23492400-23518000	Weak transcription	Esophagus	oesophagus
16	chr22:23493000-23505800	Weak transcription	Adipose Nuclei	Adipose
17	chr22:23493200-23502000	Enhancers	Placenta	Placenta
18	chr22:23493600-23505800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr22:23493600-23510800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr22:23493800-23506200	Weak transcription	Colon Smooth Muscle	Colon
21	chr22:23493800-23506200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr22:23494600-23500200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr22:23495800-23502000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr22:23495800-23504000	Weak transcription	Spleen	Spleen
25	chr22:23495800-23504800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr22:23495800-23505800	Weak transcription	Brain Angular Gyrus	brain
27	chr22:23495800-23505800	Weak transcription	Lung	lung
28	chr22:23496600-23502200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr22:23496800-23501000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr22:23496800-23501200	Weak transcription	Pancreas	Pancrea
31	chr22:23496800-23502000	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr22:23497000-23504800	Weak transcription	Fetal Brain Female	brain
33	chr22:23497000-23506000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr22:23497800-23501600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr22:23497800-23505600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr22:23498000-23501000	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr22:23498000-23503200	Weak transcription	Brain Anterior Caudate	brain
38	chr22:23498200-23501400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr22:23498400-23500000	Enhancers	H1 Cell Line	embryonic stem cell
40	chr22:23498400-23501800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr22:23498400-23505600	Weak transcription	Brain Hippocampus Middle	brain
42	chr22:23498400-23509200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr22:23498600-23499800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr22:23498600-23500200	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr22:23498600-23500200	Weak transcription	Fetal Stomach	stomach
46	chr22:23498600-23500200	Weak transcription	Ovary	ovary
47	chr22:23498600-23501200	Flanking Active TSS	HepG2	liver
48	chr22:23498600-23502600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr22:23498600-23504000	Weak transcription	Fetal Intestine Small	intestine
50	chr22:23498800-23500000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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