Variant report

Variant	rs3788356
Chromosome Location	chr22:23527610-23527611
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:23525964..23528209-chr22:23616642..23619198,2	MCF-7	breast:
2	chr22:23527308..23529049-chr9:133618404..133620705,2	K562	blood:
3	chr22:23519987..23526245-chr22:23526726..23532791,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236794	Chromatin interaction
ENSG00000186716	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10775764	0.84[ASN][1000 genomes]
rs12484280	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1807702	0.82[ASN][1000 genomes]
rs1807705	0.82[ASN][1000 genomes]
rs1807706	0.84[ASN][1000 genomes]
rs2008176	0.84[ASN][1000 genomes]
rs2071431	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071432	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071433	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071434	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2071435	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071436	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2106109	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2246716	0.81[ASN][1000 genomes]
rs2249692	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2267007	0.84[ASN][1000 genomes]
rs2267008	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267009	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267011	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2330361	0.87[ASN][1000 genomes]
rs3761418	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788357	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4552283	0.84[ASN][1000 genomes]
rs4820541	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4820542	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4822369	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55637879	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5751593	0.84[ASN][1000 genomes]
rs5751596	0.84[ASN][1000 genomes]
rs5751597	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5751598	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5751600	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5751601	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5751602	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5751603	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5751606	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5751607	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5759604	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5759607	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5759608	0.84[ASN][1000 genomes]
rs5759609	0.84[ASN][1000 genomes]
rs5759611	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5759612	0.83[ASN][1000 genomes]
rs5759613	0.84[ASN][1000 genomes]
rs5759614	0.84[ASN][1000 genomes]
rs5759615	0.84[ASN][1000 genomes]
rs5759616	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5759617	0.83[ASN][1000 genomes]
rs5759618	0.84[ASN][1000 genomes]
rs5759619	0.83[ASN][1000 genomes]
rs5759620	0.84[ASN][1000 genomes]
rs5759621	0.84[ASN][1000 genomes]
rs5759622	0.82[ASN][1000 genomes]
rs5759624	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5759628	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5759629	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5759630	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5759631	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5759635	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5759637	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5759638	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57983679	0.82[ASN][1000 genomes]
rs5996483	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60037456	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6519421	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs713617	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs713682	0.84[ASN][1000 genomes]
rs7289172	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73152631	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs737818	0.84[ASN][1000 genomes]
rs737819	0.83[ASN][1000 genomes]
rs737820	0.84[ASN][1000 genomes]
rs756633	0.84[ASN][1000 genomes]
rs768514	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8138361	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8142746	0.84[ASN][1000 genomes]
rs9608085	0.84[ASN][1000 genomes]
rs9612244	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9612251	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9612252	0.84[ASN][1000 genomes]
rs9612253	0.84[ASN][1000 genomes]
rs9624047	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9624048	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9624049	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9624050	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9624051	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3788356	BCR	Cis_1M	lymphoblastoid	RTeQTL
rs3788356	BCR///FLJ42953///LOC644165///LOC728468	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:23523600-23527800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr22:23525200-23528400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:23525600-23527800	Enhancers	Gastric	stomach
4	chr22:23525600-23530200	Enhancers	Primary B cells from peripheral blood	blood
5	chr22:23525800-23530200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr22:23525800-23530600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr22:23526000-23528200	Enhancers	Primary B cells from cord blood	blood
8	chr22:23526000-23528400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr22:23526000-23528400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr22:23526000-23528400	Enhancers	Pancreas	Pancrea
11	chr22:23526000-23529600	Enhancers	Liver	Liver
12	chr22:23526000-23530000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr22:23526000-23530000	Weak transcription	NH-A	brain
14	chr22:23526000-23535200	Weak transcription	Stomach Mucosa	stomach
15	chr22:23526000-23546000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr22:23526200-23527800	Weak transcription	Ovary	ovary
17	chr22:23526200-23529000	Enhancers	Brain Substantia Nigra	brain
18	chr22:23526200-23529600	Weak transcription	Small Intestine	intestine
19	chr22:23526200-23529600	Weak transcription	Osteobl	bone
20	chr22:23526200-23529800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr22:23526200-23530000	Weak transcription	Left Ventricle	heart
22	chr22:23526200-23530000	Weak transcription	NHDF-Ad	bronchial
23	chr22:23526200-23530000	Weak transcription	NHLF	lung
24	chr22:23526200-23530200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr22:23526200-23530200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr22:23526200-23531000	Enhancers	Adipose Nuclei	Adipose
27	chr22:23526200-23535800	Weak transcription	Aorta	Aorta
28	chr22:23526200-23546800	Weak transcription	Colonic Mucosa	Colon
29	chr22:23526400-23527800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr22:23526400-23528600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr22:23526400-23529800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr22:23526400-23529800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr22:23526400-23530200	Enhancers	Fetal Brain Male	brain
34	chr22:23526400-23535000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr22:23526400-23536000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr22:23526400-23560800	Weak transcription	A549	lung
37	chr22:23526600-23530000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr22:23526800-23527800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr22:23526800-23530200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr22:23527000-23528400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr22:23527000-23528400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr22:23527000-23530800	Genic enhancers	K562	blood
43	chr22:23527000-23535600	Strong transcription	NHEK	skin
44	chr22:23527000-23536000	Weak transcription	HMEC	breast
45	chr22:23527000-23541400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr22:23527000-23547200	Weak transcription	Fetal Kidney	kidney
47	chr22:23527200-23528000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr22:23527200-23528600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr22:23527200-23528800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr22:23527200-23529000	Genic enhancers	HUVEC	blood vessel

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