Variant report

Variant	rs4694906
Chromosome Location	chr4:48834896-48834897
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48780694..48783941-chr4:48830567..48835952,11	MCF-7	breast:
2	chr4:48780685..48782941-chr4:48832386..48835907,3	MCF-7	breast:
3	chr4:48781848..48784199-chr4:48833719..48835866,2	K562	blood:
4	chr4:48834344..48836920-chr4:48860620..48862528,2	K562	blood:
5	chr4:48746546..48749317-chr4:48834031..48835783,2	K562	blood:

Variant related genes	Relation type
ENSG00000248256	Chromatin interaction
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11727343	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11729065	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11733534	0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11734191	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11939889	0.83[EUR][1000 genomes]
rs11943219	0.83[EUR][1000 genomes]
rs12504699	0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs12512637	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12641022	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13109500	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13119414	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13141523	0.84[CEU][hapmap]
rs13141838	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13142540	0.80[CEU][hapmap]
rs13149083	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs13152270	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1463365	0.80[ASN][1000 genomes]
rs16861510	0.83[YRI][hapmap]
rs1980193	0.84[EUR][1000 genomes]
rs2085292	0.91[JPT][hapmap]
rs2102397	0.92[YRI][hapmap]
rs2176460	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2289065	0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2290516	0.90[JPT][hapmap]
rs2354938	1.00[YRI][hapmap]
rs2572345	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2572350	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2712156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712157	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712158	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2712159	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2883562	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3761729	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4694904	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4695400	0.83[EUR][1000 genomes]
rs4695401	0.83[EUR][1000 genomes]
rs4695407	0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57797824	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62310934	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6447655	0.81[EUR][1000 genomes]
rs6830078	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6830848	0.93[CEU][hapmap];0.87[CHB][hapmap];0.94[YRI][hapmap]
rs7654032	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs7657332	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs7657698	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs7660206	0.83[CHB][hapmap]
rs7665209	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7680280	0.81[EUR][1000 genomes]
rs7681070	0.81[EUR][1000 genomes]
rs7687992	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7697522	0.90[CEU][hapmap];0.96[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs796555	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap]
rs9291326	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs937889	0.90[CEU][hapmap];0.87[CHB][hapmap];0.94[YRI][hapmap]
rs9637562	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9790336	0.81[EUR][1000 genomes]
rs9997920	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[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	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
8	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
9	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4694906	MGC45416	cis	multi-tissue	Pritchard
rs4694906	OCIAD1	cis	Esophagus Muscularis	GTEx
rs4694906	SLC10A4	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48832400-48835000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:48832400-48835200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:48832600-48835000	Active TSS	H1 Cell Line	embryonic stem cell
4	chr4:48832600-48835000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:48832600-48835000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:48832800-48835200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr4:48832800-48835600	Active TSS	GM12878-XiMat	blood
8	chr4:48833000-48835000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:48833600-48835200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:48833800-48836400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:48833800-48836400	Weak transcription	Spleen	Spleen
12	chr4:48834000-48835000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:48834000-48835000	Enhancers	Primary B cells from peripheral blood	blood
14	chr4:48834000-48836200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:48834000-48836200	Weak transcription	Lung	lung
16	chr4:48834000-48836200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:48834000-48836400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:48834000-48836400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:48834000-48836400	Weak transcription	Gastric	stomach
20	chr4:48834000-48836400	Weak transcription	Pancreas	Pancrea
21	chr4:48834000-48836600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:48834000-48836600	Weak transcription	Esophagus	oesophagus
23	chr4:48834000-48859800	Weak transcription	Aorta	Aorta
24	chr4:48834000-48864600	Weak transcription	Stomach Mucosa	stomach
25	chr4:48834200-48835000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:48834200-48835000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr4:48834200-48835000	Enhancers	Primary T cells from cord blood	blood
28	chr4:48834200-48835000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr4:48834200-48835000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr4:48834200-48835000	Enhancers	Brain Cingulate Gyrus	brain
31	chr4:48834200-48835000	Enhancers	Brain Hippocampus Middle	brain
32	chr4:48834200-48835000	Enhancers	Brain Substantia Nigra	brain
33	chr4:48834200-48835400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr4:48834200-48835400	Enhancers	Colon Smooth Muscle	Colon
35	chr4:48834200-48835600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr4:48834200-48835800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr4:48834200-48836400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:48834200-48836600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:48834200-48837600	Weak transcription	Colonic Mucosa	Colon
40	chr4:48834200-48847600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr4:48834400-48835000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:48834400-48835000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr4:48834400-48835000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:48834400-48835000	Enhancers	Placenta	Placenta
45	chr4:48834400-48835000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr4:48834400-48835200	Enhancers	H9 Cell Line	embryonic stem cell
47	chr4:48834400-48835200	Enhancers	Primary T cells fromperipheralblood	blood
48	chr4:48834400-48835200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr4:48834400-48835200	Enhancers	Ovary	ovary
50	chr4:48834400-48835200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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