Variant report

Variant	rs10003273
Chromosome Location	chr4:48756537-48756538
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10008265	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10010571	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10030853	0.82[AMR][1000 genomes]
rs10049761	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10938534	0.81[AMR][1000 genomes]
rs10938537	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes]
rs11727343	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11728565	0.85[AMR][1000 genomes]
rs11733534	0.83[CEU][hapmap];0.86[CHB][hapmap];0.82[YRI][hapmap]
rs11737677	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs11939889	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11943219	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12503599	0.82[AMR][1000 genomes]
rs13108474	0.83[AMR][1000 genomes]
rs13108799	0.83[AMR][1000 genomes]
rs13113370	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13119041	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs13119414	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13119504	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13138269	0.81[AMR][1000 genomes]
rs13142540	0.92[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13149083	0.91[CEU][hapmap];0.91[CHB][hapmap];0.85[YRI][hapmap]
rs13151534	0.84[AMR][1000 genomes]
rs1507862	0.81[AMR][1000 genomes]
rs1507865	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs1517674	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1554256	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1554258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1589107	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17575720	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes]
rs17656094	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1876469	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes]
rs1980193	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2056201	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2085292	0.89[YRI][hapmap]
rs2089503	0.81[AMR][1000 genomes]
rs2102397	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2176460	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2290516	0.88[YRI][hapmap]
rs2354312	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2354314	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2354348	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2572350	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs2712156	0.82[CHB][hapmap]
rs28470767	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes]
rs34558821	0.81[AMR][1000 genomes]
rs3761729	0.82[CEU][hapmap];0.91[CHB][hapmap];0.85[YRI][hapmap]
rs4536901	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs4694904	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4694906	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs4695391	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs4695397	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4695400	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4695401	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4695407	0.95[CHB][hapmap];0.89[YRI][hapmap]
rs57797824	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62309747	0.83[ASN][1000 genomes]
rs6447645	0.81[AMR][1000 genomes]
rs6447647	0.81[AMR][1000 genomes]
rs6447651	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6447655	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6447666	0.85[YRI][hapmap]
rs6814811	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818954	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6819159	0.81[AMR][1000 genomes]
rs6830078	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6830848	0.84[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6843340	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs6856448	0.81[AMR][1000 genomes]
rs7654032	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[YRI][hapmap]
rs7657332	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7657698	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7660206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7667288	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7670939	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7679210	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes]
rs7680280	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7681070	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7682859	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7683398	0.81[AMR][1000 genomes]
rs7693461	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes]
rs7697522	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs776584	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs776591	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs796555	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs9291326	0.95[CHB][hapmap];0.89[YRI][hapmap]
rs937889	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs952289	0.81[AMR][1000 genomes]
rs955683	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9790336	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9997920	0.95[CHB][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	esv1792683	chr4:48686817-48764009	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1795181	chr4:48686817-48764009	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	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
10	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
11	esv1792281	chr4:48719424-48764009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1794245	chr4:48719424-48764009	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv1794757	chr4:48719424-48764009	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv594137	chr4:48748305-48763163	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10003273	SLC10A4	cis	lung	GTEx

Chromatin state (count:73 , 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	chr4:48742000-48758800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:48742000-48768400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:48742600-48768200	Weak transcription	Pancreas	Pancrea
5	chr4:48745000-48765200	Weak transcription	Primary B cells from cord blood	blood
6	chr4:48747200-48777200	Weak transcription	Fetal Intestine Small	intestine
7	chr4:48747400-48767800	Weak transcription	Fetal Intestine Large	intestine
8	chr4:48749000-48757200	Weak transcription	Gastric	stomach
9	chr4:48749200-48761400	Weak transcription	Thymus	Thymus
10	chr4:48749200-48768200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:48751000-48768400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:48751400-48758800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:48751600-48761400	Weak transcription	Dnd41	blood
14	chr4:48751600-48777200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:48751800-48763800	Weak transcription	Spleen	Spleen
16	chr4:48751800-48763800	Weak transcription	HSMM	muscle
17	chr4:48752000-48758000	Weak transcription	Left Ventricle	heart
18	chr4:48752000-48758000	Weak transcription	Ovary	ovary
19	chr4:48752000-48760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:48752000-48762600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr4:48752000-48767000	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:48752400-48758800	Weak transcription	Lung	lung
23	chr4:48752400-48765200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr4:48753200-48764600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr4:48754200-48759000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:48754400-48761200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr4:48754400-48763800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:48754600-48768000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:48754800-48774200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:48755000-48758400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:48755000-48758400	Weak transcription	Brain Angular Gyrus	brain
32	chr4:48755000-48758400	Weak transcription	Right Ventricle	heart
33	chr4:48755000-48758600	Weak transcription	Small Intestine	intestine
34	chr4:48755000-48758800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:48755000-48761400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr4:48755000-48763400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:48755000-48767400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:48755000-48773600	Weak transcription	Aorta	Aorta
39	chr4:48755200-48757200	Weak transcription	Brain Anterior Caudate	brain
40	chr4:48755200-48757400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr4:48755200-48757600	Weak transcription	Brain Substantia Nigra	brain
42	chr4:48755200-48758200	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:48755200-48758400	Weak transcription	Fetal Heart	heart
44	chr4:48755200-48758800	Weak transcription	Right Atrium	heart
45	chr4:48755200-48763000	Weak transcription	Psoas Muscle	Psoas
46	chr4:48755200-48763800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr4:48755200-48765200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr4:48755200-48765400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr4:48755200-48768400	Weak transcription	Fetal Thymus	thymus
50	chr4:48755200-48769400	Weak transcription	Monocytes-CD14+_RO01746	blood

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