Variant report

Variant	rs2176460
Chromosome Location	chr4:48770306-48770307
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48770305..48771971-chr4:48780871..48782395,2	K562	blood:
2	chr4:48768871..48771023-chr4:48775443..48777643,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10003273	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10008265	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10010571	0.82[ASN][1000 genomes]
rs10049761	0.82[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs10938537	0.95[JPT][hapmap]
rs11727343	0.81[EUR][1000 genomes]
rs11737677	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs11939889	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11943219	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12504699	1.00[YRI][hapmap]
rs12512637	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs12641022	0.84[EUR][1000 genomes]
rs13119041	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs13119414	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13141523	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13141838	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13142540	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1507865	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1517674	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1554256	0.82[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1554258	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1589107	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16861510	0.83[YRI][hapmap]
rs1702798	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1712767	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1712772	0.93[YRI][hapmap]
rs17575720	1.00[JPT][hapmap]
rs1876469	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs1980193	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2056201	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2102397	0.93[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap]
rs2289065	1.00[YRI][hapmap]
rs2354314	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2354348	0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap]
rs2354937	0.81[AFR][1000 genomes]
rs2354938	0.82[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2572345	0.83[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2572350	0.91[ASW][hapmap];0.89[CEU][hapmap];0.81[CHB][hapmap];0.83[MKK][hapmap];0.82[EUR][1000 genomes]
rs2712156	0.83[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2712157	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2712158	0.83[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2712159	0.84[EUR][1000 genomes]
rs28470767	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs28733443	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2883561	0.81[AFR][1000 genomes]
rs2883562	0.84[EUR][1000 genomes]
rs4694906	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4695391	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.98[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]
rs4695397	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4695400	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4695401	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4695407	0.81[CHB][hapmap]
rs57797824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62309747	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6447655	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6447660	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6814811	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6830078	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6830848	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6843340	0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs6853588	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7657332	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7657698	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7660206	0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7665209	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.83[EUR][1000 genomes]
rs7667288	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs7679210	1.00[JPT][hapmap]
rs7680280	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7681070	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7697522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs776584	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs776588	0.83[AMR][1000 genomes]
rs776591	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs776602	0.85[YRI][hapmap]
rs796555	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[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]
rs9291326	0.82[CHB][hapmap]
rs937889	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs955683	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9790336	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9997920	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS 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	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS 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	16 gene(s)	inside rSNPs	diseases
7	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2176460	SLC10A4	cis	lung	GTEx
rs2176460	OCIAD2	cis	lymphoblastoid	seeQTL
rs2176460	OCIAD1	Cis_1M	lymphoblastoid	RTeQTL
rs2176460	OCIAD2	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48731600-48779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:48747200-48777200	Weak transcription	Fetal Intestine Small	intestine
3	chr4:48751600-48777200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:48754800-48774200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:48755000-48773600	Weak transcription	Aorta	Aorta
6	chr4:48755200-48774200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr4:48755400-48775600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:48755600-48774800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:48756000-48773000	Weak transcription	HUVEC	blood vessel
10	chr4:48756000-48774800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:48756200-48774200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:48759000-48775600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:48759000-48778600	Weak transcription	Fetal Stomach	stomach
14	chr4:48759200-48775400	Weak transcription	NHEK	skin
15	chr4:48759200-48775600	Weak transcription	HMEC	breast
16	chr4:48761000-48779800	Weak transcription	Placenta	Placenta
17	chr4:48762000-48775200	Weak transcription	Fetal Lung	lung
18	chr4:48762000-48777200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:48763000-48779800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:48763800-48770400	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr4:48764000-48775000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:48764200-48770800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:48764200-48773600	Weak transcription	Right Ventricle	heart
24	chr4:48764400-48773000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr4:48764600-48774400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:48764600-48779800	Weak transcription	HSMM	muscle
27	chr4:48764800-48773600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr4:48766000-48774800	Weak transcription	Dnd41	blood
29	chr4:48766600-48779800	Weak transcription	Ovary	ovary
30	chr4:48766800-48772000	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr4:48767000-48779800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr4:48767200-48772000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:48767400-48770400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr4:48767400-48770800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:48767400-48775600	Weak transcription	Fetal Muscle Leg	muscle
36	chr4:48767800-48770400	ZNF genes & repeats	GM12878-XiMat	blood
37	chr4:48767800-48771800	Enhancers	Brain Hippocampus Middle	brain
38	chr4:48768000-48780800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr4:48768400-48770400	Enhancers	Primary T cells fromperipheralblood	blood
40	chr4:48768400-48771000	Weak transcription	Liver	Liver
41	chr4:48768600-48772800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:48768600-48773200	Weak transcription	Colon Smooth Muscle	Colon
43	chr4:48768600-48773600	Weak transcription	Psoas Muscle	Psoas
44	chr4:48768600-48774800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:48768600-48774800	Weak transcription	Small Intestine	intestine
46	chr4:48768600-48775600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:48768600-48775600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:48768600-48775600	Weak transcription	Right Atrium	heart
49	chr4:48768600-48775600	Weak transcription	Spleen	Spleen
50	chr4:48768600-48777200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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