Variant report

Variant	rs3002374
Chromosome Location	chr9:71798973-71798974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71794571..71798394-chr9:71798897..71802534,4	K562	blood:
2	chr9:71798131..71799806-chr9:71811511..71814165,2	MCF-7	breast:
3	chr9:71793542..71796888-chr9:71798932..71802737,4	MCF-7	breast:
4	chr9:71730545..71732525-chr9:71797822..71800476,2	K562	blood:
5	chr9:71790152..71792261-chr9:71797735..71799818,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10481782	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10781464	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11145615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12004488	0.81[ASN][1000 genomes]
rs12686304	0.86[ASN][1000 genomes]
rs13286409	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2252949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2486450	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2486453	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2498417	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2498420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2498435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2498440	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2498441	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2993821	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002375	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002376	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3002383	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35039239	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35066157	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35392837	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35906864	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36008762	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4237276	1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744825	1.00[CHB][hapmap]
rs4744826	1.00[CHB][hapmap]
rs4744852	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4745653	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4745688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4745693	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4745700	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018554	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7853302	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7868955	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7874185	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9411192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs946541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[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	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
6	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS 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 target site	25 gene(s)	inside rSNPs	diseases
12	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv466397	chr9:71574757-71843023	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv614550	chr9:71574757-71843023	Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv1050692	chr9:71578494-71843023	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	nsv893416	chr9:71597840-71888601	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS 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 target site	21 gene(s)	inside rSNPs	diseases
17	nsv1040539	chr9:71600042-71844108	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv540149	chr9:71600042-71844108	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	nsv949664	chr9:71607398-71842391	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription 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	20 gene(s)	inside rSNPs	diseases
20	nsv948708	chr9:71632265-71842391	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
21	nsv1037787	chr9:71635338-71807648	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
22	nsv540151	chr9:71635338-71807648	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
23	nsv817209	chr9:71675454-71829412	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
24	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
25	nsv508550	chr9:71679166-71809433	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
26	nsv893427	chr9:71762766-71858517	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3002374	RANGRF	trans	brain	seeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71790400-71832200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr9:71790400-71835600	Weak transcription	Colonic Mucosa	Colon
3	chr9:71790800-71800800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:71790800-71802200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:71791200-71802000	Weak transcription	Aorta	Aorta
6	chr9:71791200-71807600	Weak transcription	Psoas Muscle	Psoas
7	chr9:71791400-71804400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr9:71792200-71801400	Weak transcription	Fetal Kidney	kidney
9	chr9:71792200-71802400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:71792400-71808800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:71793600-71805600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:71793800-71799000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:71793800-71801000	Weak transcription	Fetal Lung	lung
14	chr9:71793800-71801200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:71794000-71806000	Weak transcription	Primary T cells from cord blood	blood
16	chr9:71794200-71801200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:71794200-71802400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr9:71795200-71801000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr9:71795600-71801000	Weak transcription	HSMMtube	muscle
20	chr9:71795600-71801200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr9:71795600-71814400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr9:71795800-71801000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:71795800-71801200	Weak transcription	Small Intestine	intestine
24	chr9:71795800-71802600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr9:71795800-71804200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr9:71795800-71806400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr9:71796000-71801000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:71796000-71801400	Weak transcription	HSMM	muscle
29	chr9:71796000-71802400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr9:71796000-71802600	Weak transcription	Gastric	stomach
31	chr9:71796000-71805600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr9:71796800-71801200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr9:71797000-71799000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:71797000-71801400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:71797000-71802400	Weak transcription	Left Ventricle	heart
36	chr9:71797000-71805800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr9:71797000-71814600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr9:71797200-71799000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr9:71797200-71799000	Weak transcription	Fetal Intestine Small	intestine
40	chr9:71797200-71799000	Weak transcription	Stomach Mucosa	stomach
41	chr9:71797200-71799200	Weak transcription	Placenta	Placenta
42	chr9:71797200-71800000	Strong transcription	Fetal Intestine Large	intestine
43	chr9:71797200-71800800	Weak transcription	Pancreas	Pancrea
44	chr9:71797200-71800800	Weak transcription	HMEC	breast
45	chr9:71797200-71801000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr9:71797200-71801000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr9:71797200-71801000	Weak transcription	Osteobl	bone
48	chr9:71797200-71801200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr9:71797200-71801200	Weak transcription	Fetal Stomach	stomach
50	chr9:71797200-71801200	Weak transcription	NH-A	brain

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