Variant report

Variant	rs17656094
Chromosome Location	chr4:48561799-48561800
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10018344	0.85[EUR][1000 genomes]
rs10029732	0.85[EUR][1000 genomes]
rs10030853	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10031777	0.85[EUR][1000 genomes]
rs10049761	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10938534	0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10938537	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11734019	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11737677	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs11933919	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11945562	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs12503599	0.84[EUR][1000 genomes]
rs12506098	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12645501	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12645951	0.81[JPT][hapmap]
rs13108474	0.85[EUR][1000 genomes]
rs13119041	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs13127730	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13138269	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13151534	0.80[EUR][1000 genomes]
rs1507862	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1507865	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1702798	0.86[EUR][1000 genomes]
rs1712767	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1712768	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1712772	0.80[CEU][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17575720	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17656010	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17656040	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17656076	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1876469	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2089503	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2102397	0.87[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap]
rs2354348	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28470767	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28733443	0.84[EUR][1000 genomes]
rs2940324	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2945330	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3107022	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34558821	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34635008	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4536901	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59686413	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62311296	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6447640	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6447645	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6447647	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6811148	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6816010	0.81[JPT][hapmap]
rs6819159	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6829144	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6829716	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6830848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[EUR][1000 genomes]
rs6836632	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs6843340	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6848073	0.82[JPT][hapmap]
rs6855022	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6856448	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7438704	0.85[JPT][hapmap]
rs7654770	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7661515	0.85[EUR][1000 genomes]
rs7667288	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7678379	0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs7679210	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7683398	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7693461	0.80[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7697522	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7697851	0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs776584	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs776588	0.83[EUR][1000 genomes]
rs776590	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs776591	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs776601	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs776602	0.85[YRI][hapmap]
rs796555	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs937888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs937889	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs952289	0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9884546	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs992423	0.87[CHB][hapmap];0.95[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17656094	SLC10A4	cis	lung	GTEx
rs17656094	OCIAD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr4:48528200-48596000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr4:48540600-48580400	Strong transcription	Fetal Intestine Large	intestine
17	chr4:48540800-48576000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr4:48541000-48580600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:48541000-48587800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr4:48541200-48566600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr4:48541200-48567000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr4:48541200-48594000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr4:48541400-48566200	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:48541400-48581200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr4:48541600-48568800	Strong transcription	Placenta	Placenta
26	chr4:48541600-48581400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:48541800-48579800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr4:48542400-48564000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:48542400-48564000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr4:48542400-48568200	Strong transcription	Brain Substantia Nigra	brain
31	chr4:48542800-48604400	Weak transcription	A549	lung
32	chr4:48544400-48566000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:48545200-48618200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:48546000-48571800	Weak transcription	Psoas Muscle	Psoas
35	chr4:48546400-48596400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr4:48546600-48578600	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr4:48547400-48578800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:48547400-48593600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr4:48549400-48563200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:48549400-48565800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:48549400-48575600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr4:48549600-48564600	Strong transcription	Fetal Muscle Leg	muscle
43	chr4:48549600-48566400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr4:48549600-48569200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:48549600-48569400	Strong transcription	Liver	Liver
46	chr4:48549600-48570200	Strong transcription	Fetal Lung	lung
47	chr4:48550000-48567800	Strong transcription	HUVEC	blood vessel
48	chr4:48550200-48568400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:48550800-48564600	Strong transcription	Primary hematopoietic stem cells	blood
50	chr4:48551000-48563600	Strong transcription	Skeletal Muscle Female	skeletal muscle

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