Variant report

Variant	rs753336
Chromosome Location	chr7:129096534-129096535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:129095996-129096764	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:129067445..129069207-chr7:129094343..129097094,2	K562	blood:
2	chr7:129009688..129011524-chr7:129096026..129097953,2	MCF-7	breast:

Variant related genes	Relation type
STRIP2	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1000676	0.84[TSI][hapmap]
rs10500117	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10954230	0.86[TSI][hapmap]
rs10954233	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10954234	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12155142	0.87[EUR][1000 genomes]
rs12540568	0.84[TSI][hapmap]
rs12667132	0.82[TSI][hapmap]
rs12667232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12671604	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34000750	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34794308	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34916100	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35131522	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35277123	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35544616	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4728163	0.91[TSI][hapmap]
rs4728164	0.86[TSI][hapmap]
rs4728165	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4731578	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4731579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731580	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4731581	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4731582	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4731583	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs598412	0.91[CHD][hapmap]
rs62489110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs644723	0.85[JPT][hapmap]
rs691124	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs691158	0.86[JPT][hapmap]
rs691435	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs691555	0.86[CHD][hapmap]
rs692697	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs6943021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966481	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428508	chr7:128946738-129114691	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1015550	chr7:128992460-129111060	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539122	chr7:128992460-129111060	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv831128	chr7:129063040-129240800	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs753336	AHCYL2	cis	parietal	SCAN
rs753336	IRF5	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129075200-129100600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:129075200-129108400	Weak transcription	Gastric	stomach
3	chr7:129075400-129102800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:129075400-129105800	Weak transcription	Ovary	ovary
5	chr7:129076000-129110000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:129077400-129109400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:129079600-129107200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr7:129079800-129106400	Weak transcription	NHDF-Ad	bronchial
9	chr7:129080000-129104800	Weak transcription	A549	lung
10	chr7:129080000-129128000	Weak transcription	HUVEC	blood vessel
11	chr7:129080600-129101800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:129082600-129108400	Weak transcription	Thymus	Thymus
13	chr7:129083800-129112800	Strong transcription	K562	blood
14	chr7:129085800-129103600	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr7:129087600-129103600	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr7:129088400-129098000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:129088800-129099800	Weak transcription	HSMMtube	muscle
18	chr7:129089200-129106600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:129089400-129099400	Weak transcription	Spleen	Spleen
20	chr7:129089400-129102600	Weak transcription	Brain Hippocampus Middle	brain
21	chr7:129089400-129108400	Weak transcription	Fetal Lung	lung
22	chr7:129089400-129110000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr7:129089600-129097800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr7:129089600-129106400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr7:129089600-129110200	Weak transcription	Brain Substantia Nigra	brain
26	chr7:129091400-129096600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr7:129091400-129097000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:129091400-129104000	Strong transcription	Brain Anterior Caudate	brain
29	chr7:129091600-129109200	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr7:129091800-129108800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr7:129092600-129109200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr7:129092800-129106800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr7:129093200-129096600	Weak transcription	Osteobl	bone
34	chr7:129093200-129109400	Weak transcription	Fetal Thymus	thymus
35	chr7:129093400-129100200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr7:129093400-129105600	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr7:129093400-129134800	Weak transcription	Right Atrium	heart
38	chr7:129093800-129096600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr7:129093800-129101600	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr7:129093800-129101800	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr7:129094000-129105200	Strong transcription	Fetal Muscle Leg	muscle
42	chr7:129094200-129097200	Strong transcription	HSMM	muscle
43	chr7:129094200-129100400	Strong transcription	HepG2	liver
44	chr7:129094200-129100600	Weak transcription	Brain Angular Gyrus	brain
45	chr7:129094400-129097200	Weak transcription	Esophagus	oesophagus
46	chr7:129094600-129097000	Strong transcription	Hela-S3	cervix
47	chr7:129094600-129102200	Weak transcription	Fetal Intestine Small	intestine
48	chr7:129094800-129098400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr7:129094800-129101000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:129094800-129104800	Strong transcription	H9 Cell Line	embryonic stem cell

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