Variant report

Variant	rs2059404
Chromosome Location	chr12:46215163-46215164
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	chr12:46213210..46215729-chr12:46383628..46386262,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139218	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1012642	0.95[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap]
rs10748432	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10880855	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10880859	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880860	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880864	0.83[EUR][1000 genomes]
rs10880871	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10880875	0.95[CEU][hapmap]
rs10880879	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap]
rs10880880	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap]
rs10880884	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs11183201	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11183210	0.80[JPT][hapmap]
rs11183243	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs11183272	0.95[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap]
rs12314770	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap]
rs12319077	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12320533	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1366024	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[TSI][hapmap]
rs1468993	0.95[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1863127	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2193749	0.95[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs2408435	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs247917	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs247918	0.90[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs247919	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs247920	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs247929	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs247930	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35115	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35117	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35121	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35122	0.91[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35125	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6582574	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67133230	0.83[EUR][1000 genomes]
rs7132422	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7138997	0.95[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs724909	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap]
rs7306229	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7315731	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7955891	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7971993	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs7976870	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs997307	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832396	chr12:46155424-46310583	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv3325128	chr12:46175148-46224560	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46149600-46215400	Weak transcription	Fetal Kidney	kidney
2	chr12:46164600-46230000	Weak transcription	Thymus	Thymus
3	chr12:46169000-46215400	Weak transcription	Fetal Lung	lung
4	chr12:46175200-46215400	Weak transcription	Primary B cells from cord blood	blood
5	chr12:46177600-46243400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:46182600-46230600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr12:46183800-46215400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:46183800-46243400	Weak transcription	Small Intestine	intestine
9	chr12:46184600-46231200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:46186000-46233400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:46186200-46215200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:46186200-46215400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:46186800-46243400	Weak transcription	HSMMtube	muscle
14	chr12:46191400-46215200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:46193200-46215600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr12:46193400-46217400	Weak transcription	K562	blood
17	chr12:46194000-46228200	Weak transcription	Fetal Stomach	stomach
18	chr12:46196400-46243200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:46198000-46215800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:46198000-46229600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:46198200-46226200	Weak transcription	Esophagus	oesophagus
22	chr12:46200600-46216400	Weak transcription	NHEK	skin
23	chr12:46200600-46244000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:46200800-46227400	Weak transcription	Fetal Intestine Small	intestine
25	chr12:46201800-46215400	Weak transcription	Liver	Liver
26	chr12:46201800-46233200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:46202000-46215200	Weak transcription	HepG2	liver
28	chr12:46202000-46215800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:46202000-46217200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:46202200-46215400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:46202200-46233200	Weak transcription	Brain Hippocampus Middle	brain
32	chr12:46202600-46221200	Weak transcription	Fetal Brain Female	brain
33	chr12:46202600-46233400	Weak transcription	Brain Substantia Nigra	brain
34	chr12:46202600-46243400	Weak transcription	Aorta	Aorta
35	chr12:46202800-46215400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:46202800-46220200	Weak transcription	Pancreas	Pancrea
37	chr12:46202800-46230400	Weak transcription	Left Ventricle	heart
38	chr12:46202800-46237800	Weak transcription	Lung	lung
39	chr12:46202800-46243200	Weak transcription	Ovary	ovary
40	chr12:46202800-46243200	Weak transcription	Right Ventricle	heart
41	chr12:46203400-46216000	Weak transcription	Fetal Muscle Leg	muscle
42	chr12:46203800-46216200	Weak transcription	NH-A	brain
43	chr12:46203800-46243800	Weak transcription	Spleen	Spleen
44	chr12:46204000-46215400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr12:46204000-46230200	Weak transcription	Brain Anterior Caudate	brain
46	chr12:46204000-46233600	Weak transcription	Psoas Muscle	Psoas
47	chr12:46204200-46217800	Weak transcription	Stomach Mucosa	stomach
48	chr12:46204200-46233200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr12:46204400-46215200	Weak transcription	Fetal Muscle Trunk	muscle
50	chr12:46205000-46230200	Weak transcription	Osteobl	bone

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