Variant report

Variant	rs7683398
Chromosome Location	chr4:48546153-48546154
allele	C/T
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	FOS	chr4:48545905-48546321	HUVEC	blood vessel:	n/a	chr4:48546081-48546092

No.	Distal block	Cell Line	Cell type
1	chr4:48544834..48546523-chr4:48551748..48553430,2	K562	blood:
2	chr4:48537925..48542072-chr4:48545238..48547735,4	MCF-7	breast:
3	chr4:48540734..48543756-chr4:48544156..48546827,3	K562	blood:
4	chr4:48544798..48547202-chr4:48547585..48550230,2	MCF-7	breast:

Variant related genes	Relation type
FRYL	TF binding region
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10003273	0.81[AMR][1000 genomes]
rs10008265	0.81[AMR][1000 genomes]
rs10018344	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10029732	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10029785	0.81[JPT][hapmap]
rs10030853	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10031777	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10049761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10938534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10938537	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11728565	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11734019	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11737677	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11933919	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11945562	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12503599	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12506098	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12645501	0.80[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12645951	0.81[JPT][hapmap]
rs13108474	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13113370	0.81[EUR][1000 genomes]
rs13119041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs13119504	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13127730	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13138269	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13151534	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1507862	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1507865	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1554258	0.81[AMR][1000 genomes]
rs1712768	0.87[EUR][1000 genomes]
rs1712772	0.82[EUR][1000 genomes]
rs17575720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17656010	0.93[ASN][1000 genomes]
rs17656040	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17656076	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17656094	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1876469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2089503	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2102397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2292231	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2354312	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2354348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28470767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2940324	0.81[EUR][1000 genomes]
rs2945330	0.85[EUR][1000 genomes]
rs3107022	0.86[EUR][1000 genomes]
rs34558821	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34635008	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs404445	0.81[JPT][hapmap]
rs411261	0.81[JPT][hapmap]
rs4536901	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4695391	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59686413	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62311296	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6447640	0.87[EUR][1000 genomes]
rs6447645	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6447647	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6447651	0.81[EUR][1000 genomes]
rs6811148	0.80[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6814811	0.81[AMR][1000 genomes]
rs6816010	0.81[JPT][hapmap]
rs6818954	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6819159	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6829716	0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs6830848	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6836632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6843340	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6848073	0.82[JPT][hapmap]
rs6855022	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6856448	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7438704	0.85[JPT][hapmap]
rs7654770	0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs7661515	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7667288	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7670939	0.81[EUR][1000 genomes]
rs7678379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7679210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7693461	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7697522	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs7697851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs776584	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs776590	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs776591	0.80[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs776601	0.87[EUR][1000 genomes]
rs796555	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs937888	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs937889	0.80[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs952289	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884546	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs992423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7683398	SLC10A4	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48498600-48593000	Strong transcription	Rectal Mucosa Donor 31	rectum
2	chr4:48499000-48578800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:48499000-48589400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr4:48499600-48581400	Strong transcription	Dnd41	blood
5	chr4:48500200-48588800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr4:48501400-48578600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr4:48504400-48575400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:48505200-48575400	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr4:48507200-48564000	Strong transcription	Fetal Thymus	thymus
10	chr4:48507600-48568600	Strong transcription	Primary T cells from cord blood	blood
11	chr4:48515800-48625000	Weak transcription	Hela-S3	cervix
12	chr4:48519400-48566200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr4:48522600-48563200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:48525000-48595600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:48525200-48552800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:48528200-48596000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:48533000-48552600	Weak transcription	Aorta	Aorta
18	chr4:48533600-48547000	Weak transcription	Fetal Brain Male	brain
19	chr4:48535000-48548600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:48538600-48547200	Weak transcription	NHLF	lung
21	chr4:48540600-48580400	Strong transcription	Fetal Intestine Large	intestine
22	chr4:48540800-48550200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:48540800-48576000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr4:48541000-48580600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:48541000-48587800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr4:48541200-48548200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:48541200-48548400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:48541200-48548600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:48541200-48548600	Strong transcription	Primary hematopoietic stem cells	blood
30	chr4:48541200-48553600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:48541200-48560000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:48541200-48566600	Strong transcription	Primary B cells from peripheral blood	blood
33	chr4:48541200-48567000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:48541200-48594000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr4:48541400-48548200	Strong transcription	Rectal Smooth Muscle	rectum
36	chr4:48541400-48548400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:48541400-48548400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:48541400-48548600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr4:48541400-48548600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr4:48541400-48548600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:48541400-48548600	Strong transcription	Fetal Lung	lung
42	chr4:48541400-48554400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr4:48541400-48554400	Strong transcription	Brain Hippocampus Middle	brain
44	chr4:48541400-48555800	Strong transcription	Primary B cells from cord blood	blood
45	chr4:48541400-48566200	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr4:48541400-48581200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr4:48541600-48548400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:48541600-48548400	Strong transcription	NHEK	skin
49	chr4:48541600-48548600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr4:48541600-48548600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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