Variant report

Variant	rs6447655
Chromosome Location	chr4:48729252-48729253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48720217..48721926-chr4:48727442..48730398,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10003273	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10008265	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10049761	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10938537	0.95[JPT][hapmap]
rs11727343	0.82[CEU][hapmap]
rs11737677	1.00[JPT][hapmap]
rs11939889	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11943219	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12512637	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs12641022	0.81[EUR][1000 genomes]
rs13113370	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13119041	1.00[JPT][hapmap]
rs13119414	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13119504	0.80[ASN][1000 genomes]
rs13141838	0.86[EUR][1000 genomes]
rs13142540	0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1507865	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1517674	0.80[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1554256	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1554258	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1589107	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16861510	0.83[YRI][hapmap]
rs1702798	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1712767	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1712772	0.80[CEU][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17575720	1.00[JPT][hapmap]
rs17656040	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17656094	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1876469	1.00[JPT][hapmap]
rs1980193	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2056201	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2102397	0.91[JPT][hapmap];0.92[YRI][hapmap]
rs2176460	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2289065	1.00[YRI][hapmap]
rs2354314	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2354348	0.95[JPT][hapmap]
rs2354938	1.00[YRI][hapmap]
rs2572345	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2572350	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs2712156	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2712158	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2712159	0.81[EUR][1000 genomes]
rs28470767	1.00[JPT][hapmap]
rs28733443	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2883562	0.81[EUR][1000 genomes]
rs2940324	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3107022	0.80[AFR][1000 genomes]
rs4536901	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4694906	0.93[CEU][hapmap];0.96[CHB][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs4695391	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4695397	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4695400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4695401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4695407	0.82[CHB][hapmap]
rs57797824	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62309747	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6447651	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6447660	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6814811	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6830078	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6830848	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6843340	1.00[JPT][hapmap]
rs6853588	0.84[EUR][1000 genomes]
rs7654032	0.80[CEU][hapmap]
rs7657332	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7657698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7660206	0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7665209	0.92[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs7667288	1.00[JPT][hapmap]
rs7670939	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7679210	1.00[JPT][hapmap]
rs7680280	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7681070	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7682859	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7683398	1.00[JPT][hapmap]
rs7693461	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs7697522	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs776584	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs776588	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs776591	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs776602	0.85[YRI][hapmap]
rs796555	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9291326	0.82[CHB][hapmap]
rs937888	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs937889	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs952289	1.00[JPT][hapmap]
rs955683	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9790336	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9997920	0.82[CHB][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	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	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
9	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
10	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
11	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
12	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
13	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
14	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6447655	SLC10A4	cis	lung	GTEx
rs6447655	OCIAD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48621200-48729400	Weak transcription	Thymus	Thymus
2	chr4:48700200-48730800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:48701000-48729600	Weak transcription	Aorta	Aorta
4	chr4:48712800-48731000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:48720000-48737000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:48720200-48730000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:48721000-48729400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr4:48721200-48730800	Weak transcription	Fetal Intestine Small	intestine
9	chr4:48721400-48729400	Weak transcription	Right Atrium	heart
10	chr4:48721400-48729600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:48724000-48731800	Enhancers	Brain Hippocampus Middle	brain
12	chr4:48724400-48732800	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr4:48724800-48731000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr4:48725400-48729400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:48725400-48731200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:48725600-48730800	Weak transcription	Gastric	stomach
17	chr4:48725600-48731200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:48725800-48729400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:48725800-48729600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:48725800-48729800	Weak transcription	Dnd41	blood
21	chr4:48726400-48730800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr4:48726400-48730800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr4:48727200-48730000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:48727200-48732200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr4:48727400-48731600	Enhancers	Brain Substantia Nigra	brain
26	chr4:48727400-48732400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:48727600-48730200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:48727600-48730200	Enhancers	HUVEC	blood vessel
29	chr4:48727600-48733600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr4:48727800-48729400	Enhancers	Brain Cingulate Gyrus	brain
31	chr4:48727800-48730200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:48727800-48730400	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr4:48727800-48731000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:48727800-48731000	Weak transcription	Esophagus	oesophagus
35	chr4:48727800-48731400	Enhancers	HMEC	breast
36	chr4:48727800-48732600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr4:48728000-48730000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr4:48728000-48730000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:48728000-48731000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:48728000-48731600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr4:48728200-48729400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:48728200-48729400	Weak transcription	Primary T cells from cord blood	blood
43	chr4:48728200-48729400	Weak transcription	Right Ventricle	heart
44	chr4:48728200-48729800	Enhancers	GM12878-XiMat	blood
45	chr4:48728200-48730000	Enhancers	HepG2	liver
46	chr4:48728200-48730200	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr4:48728200-48730200	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr4:48728200-48731000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:48728200-48731400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:48728400-48729400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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