Variant report

Variant	rs13140054
Chromosome Location	chr4:147209404-147209405
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	chr4:147209226..147212026-chr4:147214111..147217530,3	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10022940	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10050271	0.85[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs10212747	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1030777	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10519783	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11100922	0.85[CEU][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes]
rs12645587	0.81[AMR][1000 genomes]
rs12711434	0.92[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13109522	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13116650	0.82[AMR][1000 genomes]
rs13117626	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13143634	0.83[CEU][hapmap];0.87[AMR][1000 genomes]
rs1485953	0.86[CEU][hapmap];0.87[AMR][1000 genomes]
rs17828118	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960018	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991978	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062436	0.81[CEU][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs2062437	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062438	0.85[CEU][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes]
rs2163170	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4103543	0.85[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes]
rs4835291	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537411	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6537414	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6537417	0.85[CEU][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs6813017	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6844812	0.85[CEU][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes]
rs6849067	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7661938	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7689364	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs7693289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923166	0.83[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs962628	0.85[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes]
rs9991483	0.82[CEU][hapmap];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3332743	chr4:147204602-147209500	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147167000-147217600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:147174400-147231200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:147174800-147218400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr4:147175400-147225400	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:147177400-147213400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr4:147179400-147217200	Weak transcription	Left Ventricle	heart
7	chr4:147179600-147214200	Weak transcription	Dnd41	blood
8	chr4:147180400-147233200	Weak transcription	Liver	Liver
9	chr4:147186600-147212800	Weak transcription	Psoas Muscle	Psoas
10	chr4:147188400-147215200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr4:147197400-147213200	Weak transcription	K562	blood
12	chr4:147198000-147224000	Weak transcription	Fetal Intestine Small	intestine
13	chr4:147201000-147224800	Weak transcription	HMEC	breast
14	chr4:147201000-147225400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:147201000-147249600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:147201600-147209600	Weak transcription	NH-A	brain
17	chr4:147201600-147214600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr4:147204000-147220800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:147204200-147211400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:147204600-147209800	Weak transcription	Brain Substantia Nigra	brain
21	chr4:147205600-147211600	Weak transcription	GM12878-XiMat	blood
22	chr4:147205600-147214000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:147205800-147217600	Weak transcription	Fetal Brain Female	brain
24	chr4:147206000-147216400	Weak transcription	Colon Smooth Muscle	Colon
25	chr4:147206200-147213800	Weak transcription	Placenta	Placenta
26	chr4:147206200-147217600	Weak transcription	Fetal Brain Male	brain
27	chr4:147206200-147225400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:147206400-147210200	Strong transcription	Primary T cells from cord blood	blood
29	chr4:147206800-147209800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr4:147206800-147210600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:147206800-147218000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:147207200-147209600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr4:147207400-147209600	Strong transcription	Stomach Smooth Muscle	stomach
34	chr4:147207600-147213000	Weak transcription	HSMM	muscle
35	chr4:147207600-147216600	Weak transcription	Fetal Muscle Leg	muscle
36	chr4:147207600-147226600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:147208200-147209800	Weak transcription	Brain Angular Gyrus	brain
38	chr4:147208200-147209800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr4:147208200-147211800	Weak transcription	Fetal Intestine Large	intestine
40	chr4:147208200-147211800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr4:147208200-147212200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr4:147208200-147212200	Weak transcription	Thymus	Thymus
43	chr4:147208200-147213800	Weak transcription	Spleen	Spleen
44	chr4:147208200-147217000	Weak transcription	Fetal Kidney	kidney
45	chr4:147208200-147219200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr4:147208200-147220600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr4:147208200-147232800	Weak transcription	Aorta	Aorta
48	chr4:147208200-147234200	Weak transcription	Lung	lung
49	chr4:147208200-147247000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr4:147208400-147210800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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