Variant report

Variant	rs6830848
Chromosome Location	chr4:48690408-48690409
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	chr4:48689702..48692594-chr4:48697555..48699219,2	K562	blood:
2	chr4:48689938..48695241-chr4:48778784..48782766,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10003273	0.81[ASN][1000 genomes]
rs10049761	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10938534	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs10938537	0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs11727343	0.82[CEU][hapmap]
rs11728565	0.80[EUR][1000 genomes]
rs11737677	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs11939889	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11943219	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12506098	0.81[EUR][1000 genomes]
rs12512637	0.92[CEU][hapmap];0.82[CHB][hapmap];0.94[YRI][hapmap]
rs12645501	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs13113370	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13119041	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs13119414	0.85[EUR][1000 genomes]
rs13119504	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13142540	1.00[JPT][hapmap]
rs1507865	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs1517674	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs1554256	1.00[JPT][hapmap]
rs16861510	0.83[YRI][hapmap]
rs1702798	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1712767	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1712768	0.82[EUR][1000 genomes]
rs1712772	0.80[CEU][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17575720	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs17656040	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs17656076	0.83[EUR][1000 genomes]
rs17656094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[EUR][1000 genomes]
rs1876469	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1980193	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2102397	0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs2176460	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]
rs2354312	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2354314	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2354348	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2354938	0.92[YRI][hapmap]
rs2572345	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[YRI][hapmap]
rs2572350	0.85[CEU][hapmap]
rs2712156	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[YRI][hapmap]
rs2712158	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs28470767	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs28733443	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2940324	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3107022	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34635008	0.83[EUR][1000 genomes]
rs4536901	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs4694906	0.93[CEU][hapmap];0.87[CHB][hapmap];0.94[YRI][hapmap]
rs4695391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs4695397	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4695400	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4695401	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57797824	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59686413	0.83[EUR][1000 genomes]
rs62309747	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62311296	0.81[EUR][1000 genomes]
rs6447651	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6447655	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6811148	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[EUR][1000 genomes]
rs6814811	0.81[ASN][1000 genomes]
rs6818954	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6830078	0.83[EUR][1000 genomes]
rs6843340	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6855022	0.82[EUR][1000 genomes]
rs7654032	0.80[CEU][hapmap]
rs7657332	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7657698	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7660206	1.00[JPT][hapmap]
rs7665209	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs7667288	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7670939	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7679210	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7680280	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7681070	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7682859	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7683398	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7693461	0.80[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7697522	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs776584	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs776588	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs776590	0.83[EUR][1000 genomes]
rs776591	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[EUR][1000 genomes]
rs776601	0.83[EUR][1000 genomes]
rs796555	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs937888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs937889	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs952289	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs955683	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9790336	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv999203	chr4:48645887-48735512	Enhancers Weak transcription Flanking Active TSS Strong transcription 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	esv1802666	chr4:48646594-48721327	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1013914	chr4:48652784-48728934	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv537090	chr4:48652784-48728934	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription 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
11	esv1796692	chr4:48686817-48726266	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6830848	OCIAD1	Cis_1M	lymphoblastoid	RTeQTL
rs6830848	SLC10A4	cis	lung	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48621200-48729400	Weak transcription	Thymus	Thymus
2	chr4:48663600-48700200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:48670000-48691000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:48670200-48700000	Weak transcription	Esophagus	oesophagus
5	chr4:48670200-48702000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr4:48670200-48702000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:48670400-48696000	Weak transcription	Left Ventricle	heart
8	chr4:48671400-48696000	Weak transcription	Right Ventricle	heart
9	chr4:48679000-48700000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:48680200-48692800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:48680600-48699600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:48683200-48691000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:48683400-48699600	Weak transcription	Psoas Muscle	Psoas
14	chr4:48683600-48692400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr4:48683600-48700000	Weak transcription	Fetal Intestine Large	intestine
16	chr4:48683600-48700400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr4:48684000-48698400	Weak transcription	NHEK	skin
18	chr4:48684200-48695400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr4:48685000-48700400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:48686400-48694200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr4:48686400-48699600	Weak transcription	Placenta	Placenta
22	chr4:48686400-48700000	Weak transcription	Dnd41	blood
23	chr4:48686600-48693200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:48686600-48694000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:48686600-48694200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr4:48686800-48695000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr4:48686800-48700200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:48686800-48708800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:48687000-48691000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr4:48687000-48693400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr4:48687000-48700000	Weak transcription	Primary B cells from peripheral blood	blood
32	chr4:48687000-48700000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr4:48687000-48701000	Weak transcription	GM12878-XiMat	blood
34	chr4:48687000-48708400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr4:48687200-48700000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:48687200-48708400	Weak transcription	Primary B cells from cord blood	blood
37	chr4:48687800-48691000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr4:48688800-48696000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:48689000-48694200	Weak transcription	Brain Angular Gyrus	brain
40	chr4:48689400-48693000	Weak transcription	Fetal Kidney	kidney
41	chr4:48689600-48690600	Flanking Active TSS	K562	blood
42	chr4:48689800-48690800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:48689800-48691000	Weak transcription	HSMM	muscle
44	chr4:48689800-48692600	Weak transcription	Brain Substantia Nigra	brain
45	chr4:48689800-48694200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:48689800-48694400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:48690000-48691400	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr4:48690000-48693000	Weak transcription	Brain Anterior Caudate	brain
49	chr4:48690000-48693000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:48690000-48693600	Weak transcription	Brain Cingulate Gyrus	brain

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