Variant report

Variant	rs11939889
Chromosome Location	chr4:48758219-48758220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48756947..48759205-chr4:48760988..48763771,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10003273	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10008265	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11727343	0.80[EUR][1000 genomes]
rs11943219	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12512637	0.83[EUR][1000 genomes]
rs12641022	0.83[EUR][1000 genomes]
rs13113370	0.85[ASN][1000 genomes]
rs13119414	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13141838	0.87[EUR][1000 genomes]
rs13142540	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1517674	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1554256	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1554258	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1589107	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1702798	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1712767	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1980193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2056201	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2176460	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2354314	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2572345	0.83[EUR][1000 genomes]
rs2572350	0.81[EUR][1000 genomes]
rs2712156	0.83[EUR][1000 genomes]
rs2712157	0.81[EUR][1000 genomes]
rs2712158	0.83[EUR][1000 genomes]
rs2712159	0.83[EUR][1000 genomes]
rs28733443	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2883562	0.83[EUR][1000 genomes]
rs4694906	0.83[EUR][1000 genomes]
rs4695397	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4695400	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4695401	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57797824	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62309747	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6447651	0.87[ASN][1000 genomes]
rs6447655	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6447660	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6814811	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6830078	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6830848	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6853588	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7657332	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7657698	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7660206	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7665209	0.82[EUR][1000 genomes]
rs7670939	0.87[ASN][1000 genomes]
rs7680280	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7681070	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7682859	0.87[ASN][1000 genomes]
rs7697522	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs776588	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs955683	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9790336	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11939889	SLC10A4	cis	lung	GTEx
rs11939889	OCIAD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 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	chr4:48749200-48761400	Weak transcription	Thymus	Thymus
9	chr4:48749200-48768200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:48751000-48768400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:48751400-48758800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:48751600-48761400	Weak transcription	Dnd41	blood
13	chr4:48751600-48777200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:48751800-48763800	Weak transcription	Spleen	Spleen
15	chr4:48751800-48763800	Weak transcription	HSMM	muscle
16	chr4:48752000-48760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:48752000-48762600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:48752000-48767000	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:48752400-48758800	Weak transcription	Lung	lung
20	chr4:48752400-48765200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr4:48753200-48764600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr4:48754200-48759000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:48754400-48761200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:48754400-48763800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:48754600-48768000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:48754800-48774200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:48755000-48758400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:48755000-48758400	Weak transcription	Brain Angular Gyrus	brain
29	chr4:48755000-48758400	Weak transcription	Right Ventricle	heart
30	chr4:48755000-48758600	Weak transcription	Small Intestine	intestine
31	chr4:48755000-48758800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:48755000-48761400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr4:48755000-48763400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:48755000-48767400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:48755000-48773600	Weak transcription	Aorta	Aorta
36	chr4:48755200-48758400	Weak transcription	Fetal Heart	heart
37	chr4:48755200-48758800	Weak transcription	Right Atrium	heart
38	chr4:48755200-48763000	Weak transcription	Psoas Muscle	Psoas
39	chr4:48755200-48763800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr4:48755200-48765200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr4:48755200-48765400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr4:48755200-48768400	Weak transcription	Fetal Thymus	thymus
43	chr4:48755200-48769400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr4:48755200-48774200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr4:48755400-48759200	Weak transcription	NHDF-Ad	bronchial
46	chr4:48755400-48763600	Weak transcription	Osteobl	bone
47	chr4:48755400-48763800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:48755400-48763800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr4:48755400-48768200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:48755400-48775600	Weak transcription	Rectal Mucosa Donor 31	rectum

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