Variant report

Variant	rs7613579
Chromosome Location	chr3:138568591-138568592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138552298..138556621-chr3:138563607..138569226,8	K562	blood:
2	chr3:138552479..138554870-chr3:138567696..138569343,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000051382	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10804659	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10935288	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706016	0.96[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11708762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711360	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720178	0.96[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs11924479	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924939	1.00[CHB][hapmap]
rs12497815	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633714	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12635713	0.87[EUR][1000 genomes]
rs13061496	0.96[CEU][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13072146	0.91[EUR][1000 genomes]
rs13077455	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080973	1.00[CHB][hapmap]
rs13100110	0.88[EUR][1000 genomes]
rs1663554	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs1673597	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs17484361	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17485052	1.00[CHB][hapmap]
rs17548850	1.00[CHB][hapmap]
rs191714	0.96[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs191775	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs2881900	0.96[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361059	0.96[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs361060	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs361061	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs361062	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs361063	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs361066	0.96[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs361067	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs361071	0.96[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs361072	0.96[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs361080	0.96[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs361082	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs361087	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs361088	0.96[CEU][hapmap]
rs361096	0.88[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs385254	0.96[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs413147	0.96[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs4305444	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs4405948	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894358	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493152	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs497900	0.96[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs500687	0.96[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs520904	0.96[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs524164	0.96[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs531577	0.88[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs558905	0.96[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs559160	0.96[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs564455	0.96[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs603723	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs62282204	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62282207	0.85[EUR][1000 genomes]
rs624099	0.96[CEU][hapmap]
rs635592	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs6439817	0.96[CEU][hapmap]
rs6439828	0.81[CEU][hapmap]
rs6773514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776833	0.82[EUR][1000 genomes]
rs6780989	1.00[ASN][1000 genomes]
rs6784610	0.96[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791627	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794270	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800801	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628172	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7634571	0.81[EUR][1000 genomes]
rs7643722	0.96[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs7646689	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs773045	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs9289566	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9647336	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9647337	0.96[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813576	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817727	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818354	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9821694	0.96[CEU][hapmap]
rs9822500	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9822714	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs9834963	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs9851887	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9855727	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9871842	0.82[EUR][1000 genomes]
rs9877108	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879784	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs9882957	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv1000927	chr3:138423543-138632596	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	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
rs7613579	ESYT3	cis	cerebellum	SCAN
rs7613579	FAIM	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138565800-138568600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:138565800-138568800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:138565800-138571800	Weak transcription	NHEK	skin
4	chr3:138565800-138573200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:138566000-138568600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:138566200-138568600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:138566400-138571800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:138567400-138569200	Enhancers	Fetal Intestine Large	intestine
9	chr3:138567400-138569200	Enhancers	Fetal Intestine Small	intestine
10	chr3:138567400-138569400	Enhancers	HepG2	liver
11	chr3:138567600-138569000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:138567800-138569000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:138568000-138568800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:138568000-138568800	Enhancers	Brain Germinal Matrix	brain
15	chr3:138568200-138568800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr3:138568200-138568800	Enhancers	Adipose Nuclei	Adipose
17	chr3:138568200-138569400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr3:138568400-138568800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:138568400-138568800	Enhancers	H9 Cell Line	embryonic stem cell
20	chr3:138568400-138568800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr3:138568400-138568800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:138568400-138569000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr3:138568400-138569000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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