Variant report

Variant	rs3735141
Chromosome Location	chr7:65420340-65420341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65419413..65421834-chr7:65450885..65452622,2	K562	blood:
2	chr7:65419004..65421368-chr7:65431133..65432952,3	K562	blood:
3	chr7:65418223..65420511-chr7:65422513..65424298,2	K562	blood:
4	chr7:65419242..65420839-chr7:65426993..65428588,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169919	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs12530898	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs12531358	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12532327	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12534109	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12535985	1.00[AFR][1000 genomes]
rs12537936	1.00[AFR][1000 genomes]
rs12538025	1.00[AFR][1000 genomes]
rs2279904	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2292936	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes]
rs2292937	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes]
rs35832738	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62465474	1.00[AFR][1000 genomes]
rs62465475	1.00[AFR][1000 genomes]
rs62465476	1.00[AFR][1000 genomes]
rs62465483	1.00[AFR][1000 genomes]
rs62465484	1.00[AFR][1000 genomes]
rs62465512	1.00[AFR][1000 genomes]
rs62465513	1.00[AFR][1000 genomes]
rs62465515	1.00[AFR][1000 genomes]
rs62467382	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62467384	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62467385	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62467386	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62467387	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62467410	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62467411	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62467413	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62467414	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62467421	1.00[AFR][1000 genomes]
rs62467437	1.00[AFR][1000 genomes]
rs62467450	1.00[AFR][1000 genomes]
rs62469938	0.82[EUR][1000 genomes]
rs62469939	0.87[EUR][1000 genomes]
rs62469940	0.87[EUR][1000 genomes]
rs62470862	0.87[EUR][1000 genomes]
rs62470863	0.87[EUR][1000 genomes]
rs62470864	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62470868	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62470870	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62470879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62470880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62470883	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62470884	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62470886	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62470891	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62470894	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62470895	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62470897	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62470899	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62470900	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62470921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470931	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470932	0.82[EUR][1000 genomes]
rs62470934	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470938	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62470940	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62470944	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62470945	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1020337	chr7:65371505-65449654	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
4	nsv1025494	chr7:65402301-65515606	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv538906	chr7:65402301-65515606	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv888321	chr7:65408904-65449541	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	esv9823	chr7:65413362-65468020	Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	esv3426468	chr7:65413488-65462982	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	esv3433491	chr7:65414034-65463477	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	nsv1028971	chr7:65414064-65457437	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
11	nsv966831	chr7:65415065-65428348	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv888322	chr7:65415647-65466565	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	nsv538907	chr7:65417400-65456089	Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
14	nsv888323	chr7:65418355-65461080	ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
15	nsv888324	chr7:65418876-65466565	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3735141	hmm32897	cis	multi-tissue	Pritchard
rs3735141	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL
rs3735141	RABGEF1	cis	lymphoblastoid	seeQTL
rs3735141	RABGEF1	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65373800-65424000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:65382000-65420600	Weak transcription	Primary B cells from cord blood	blood
3	chr7:65389400-65423800	Weak transcription	Aorta	Aorta
4	chr7:65390600-65423800	Weak transcription	Gastric	stomach
5	chr7:65395600-65420400	Weak transcription	Esophagus	oesophagus
6	chr7:65399200-65425000	Weak transcription	Small Intestine	intestine
7	chr7:65401200-65423800	Weak transcription	Spleen	Spleen
8	chr7:65401400-65425000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr7:65401800-65425000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:65402000-65424800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:65402000-65425000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr7:65404000-65420400	Weak transcription	HSMM	muscle
13	chr7:65405600-65423800	Weak transcription	Psoas Muscle	Psoas
14	chr7:65411600-65424800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr7:65412000-65423600	Weak transcription	Right Ventricle	heart
16	chr7:65412200-65423000	Weak transcription	NH-A	brain
17	chr7:65412200-65423200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr7:65412200-65425000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:65412200-65428200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:65412400-65421000	Weak transcription	HMEC	breast
21	chr7:65413200-65420400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:65413200-65420400	Weak transcription	Brain Anterior Caudate	brain
23	chr7:65413200-65420600	Weak transcription	Ovary	ovary
24	chr7:65416000-65425000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr7:65416600-65421800	Enhancers	Liver	Liver
26	chr7:65416600-65425000	Weak transcription	NHLF	lung
27	chr7:65417200-65424600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr7:65417400-65425000	Weak transcription	Colon Smooth Muscle	Colon
29	chr7:65417600-65425000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr7:65417600-65425000	Weak transcription	Brain Angular Gyrus	brain
31	chr7:65417600-65425000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr7:65417600-65425000	Weak transcription	Fetal Kidney	kidney
33	chr7:65417800-65420400	Weak transcription	Brain Substantia Nigra	brain
34	chr7:65417800-65423600	Weak transcription	Hela-S3	cervix
35	chr7:65417800-65432400	Weak transcription	Stomach Mucosa	stomach
36	chr7:65417800-65441600	Strong transcription	Primary T cells from cord blood	blood
37	chr7:65417800-65445400	Weak transcription	Fetal Heart	heart
38	chr7:65418000-65421400	Strong transcription	Fetal Stomach	stomach
39	chr7:65418000-65425000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr7:65418000-65445400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr7:65418200-65421400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr7:65418200-65424800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr7:65418200-65434400	Strong transcription	A549	lung
44	chr7:65418400-65421000	Strong transcription	NHEK	skin
45	chr7:65418400-65423800	Strong transcription	K562	blood
46	chr7:65418400-65442400	Strong transcription	Adipose Nuclei	Adipose
47	chr7:65418400-65445200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:65418600-65420400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr7:65418600-65422000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr7:65418800-65420800	Strong transcription	H1 Cell Line	embryonic stem cell

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