Variant report

Variant	rs2301555
Chromosome Location	chr22:23494904-23494905
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:23488468..23492750-chr22:23493638..23496151,4	MCF-7	breast:
2	chr22:23493765..23495502-chr22:23500270..23503203,2	MCF-7	breast:
3	chr22:23494056..23496590-chr22:23496723..23499466,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100228	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10775764	0.86[ASN][1000 genomes]
rs12167308	0.95[CHB][hapmap]
rs1807460	0.90[CHB][hapmap]
rs1807702	0.85[ASN][1000 genomes]
rs1807705	0.84[ASN][1000 genomes]
rs1807706	0.86[ASN][1000 genomes]
rs2008176	0.86[ASN][1000 genomes]
rs2106109	0.85[ASN][1000 genomes]
rs2246716	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2249692	0.80[CHB][hapmap];0.85[ASN][1000 genomes]
rs2267007	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs2330361	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs3761418	0.90[CHB][hapmap]
rs4552283	0.86[ASN][1000 genomes]
rs4820541	0.90[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs4822369	0.90[CHB][hapmap]
rs5751593	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs5751596	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs5751603	0.80[CHB][hapmap]
rs5759603	0.88[CHD][hapmap];0.80[JPT][hapmap];0.80[LWK][hapmap]
rs5759604	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs5759607	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs5759608	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs5759609	0.86[ASN][1000 genomes]
rs5759611	0.90[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs5759612	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs5759613	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs5759614	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs5759615	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs5759616	0.81[ASN][1000 genomes]
rs5759617	0.86[ASN][1000 genomes]
rs5759618	0.86[ASN][1000 genomes]
rs5759619	1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs5759620	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs5759621	1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs5759622	0.85[ASN][1000 genomes]
rs5759631	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs57983679	0.82[ASN][1000 genomes]
rs713682	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs737818	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs737819	1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs737820	0.86[ASN][1000 genomes]
rs756633	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs8142746	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs9608085	0.86[ASN][1000 genomes]
rs9612244	0.85[ASN][1000 genomes]
rs9612251	0.84[ASN][1000 genomes]
rs9612252	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs9612253	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1803110	chr22:22731758-23497674	Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	esv34158	chr22:23216762-23499513	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
25	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
26	nsv544616	chr22:23474827-23495231	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2301555	ZNF74	cis	cerebellum	SCAN
rs2301555	SUSD2	cis	parietal	SCAN
rs2301555	ZNF70	cis	parietal	SCAN
rs2301555	BCR	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:23487800-23499000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr22:23488000-23499400	Weak transcription	Right Ventricle	heart
3	chr22:23488200-23505800	Weak transcription	HSMMtube	muscle
4	chr22:23488400-23495000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr22:23488400-23499000	Weak transcription	Colonic Mucosa	Colon
6	chr22:23488400-23499000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr22:23488400-23499200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr22:23488400-23505800	Weak transcription	Brain Substantia Nigra	brain
9	chr22:23488600-23505800	Weak transcription	Brain Germinal Matrix	brain
10	chr22:23488600-23506800	Weak transcription	A549	lung
11	chr22:23488800-23505400	Weak transcription	Fetal Brain Male	brain
12	chr22:23489000-23496400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr22:23489200-23497400	Weak transcription	Fetal Kidney	kidney
14	chr22:23489200-23499800	Weak transcription	NHLF	lung
15	chr22:23489800-23498400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:23490200-23496800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr22:23490200-23500200	Weak transcription	Fetal Lung	lung
18	chr22:23490200-23504800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr22:23490400-23498400	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr22:23490400-23499000	Weak transcription	Stomach Mucosa	stomach
21	chr22:23490400-23506800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr22:23490400-23522000	Weak transcription	Aorta	Aorta
23	chr22:23490600-23498600	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr22:23491000-23498000	Weak transcription	Gastric	stomach
25	chr22:23491000-23504600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr22:23491200-23512000	Strong transcription	Right Atrium	heart
27	chr22:23491800-23499400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr22:23492000-23495800	Strong transcription	Brain Cingulate Gyrus	brain
29	chr22:23492200-23496600	Strong transcription	Brain Hippocampus Middle	brain
30	chr22:23492200-23505800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr22:23492400-23495800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr22:23492400-23496200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr22:23492400-23496400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr22:23492400-23496400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr22:23492400-23496400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr22:23492400-23496600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr22:23492400-23498200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr22:23492400-23498600	Strong transcription	Fetal Stomach	stomach
39	chr22:23492400-23509000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr22:23492400-23518000	Weak transcription	Esophagus	oesophagus
41	chr22:23492800-23495200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr22:23492800-23496800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr22:23493000-23495800	Enhancers	Lung	lung
44	chr22:23493000-23505800	Weak transcription	Adipose Nuclei	Adipose
45	chr22:23493200-23498400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr22:23493200-23502000	Enhancers	Placenta	Placenta
47	chr22:23493400-23495200	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr22:23493400-23495800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr22:23493400-23496000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr22:23493400-23497000	Strong transcription	Fetal Brain Female	brain

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