Variant report

Variant	rs12138621
Chromosome Location	chr1:85783970-85783971
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	chr1:85783416..85785101-chr1:85792646..85795360,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10158674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10782550	0.85[ASN][1000 genomes]
rs11161597	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161614	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs11161616	0.80[CEU][hapmap]
rs11161617	0.80[CEU][hapmap]
rs11801146	0.82[ASN][1000 genomes]
rs12118950	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12120551	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12122816	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123745	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12125900	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12128907	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12129502	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12130145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12130380	0.81[CEU][hapmap]
rs12130591	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12132677	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12133722	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12135333	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12138852	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12139958	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12140170	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12140272	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140457	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12140935	1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12717763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12724823	0.95[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs12736004	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12743049	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12758237	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12758768	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1498373	1.00[YRI][hapmap]
rs1498374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1608536	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17384381	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17388521	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2076699	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2300634	1.00[YRI][hapmap]
rs2300639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2300640	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28529751	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34561661	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35193119	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35240561	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35761966	0.90[ASN][1000 genomes]
rs36110608	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3768223	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3768227	1.00[YRI][hapmap]
rs71652696	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs761601	1.00[YRI][hapmap]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85774600-85785200	Weak transcription	Liver	Liver
2	chr1:85774600-85785800	Weak transcription	Fetal Intestine Large	intestine
3	chr1:85774600-85787000	Weak transcription	Fetal Stomach	stomach
4	chr1:85774600-85794800	Weak transcription	Spleen	Spleen
5	chr1:85774800-85784000	Weak transcription	HepG2	liver
6	chr1:85774800-85790400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:85774800-85790600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:85774800-85794200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:85777400-85786400	Enhancers	NHLF	lung
10	chr1:85777600-85784000	Enhancers	NHDF-Ad	bronchial
11	chr1:85778200-85790400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:85778400-85785600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:85778800-85786000	Enhancers	NHEK	skin
14	chr1:85778800-85788800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:85778800-85789600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:85779000-85785600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:85779600-85787400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:85780000-85791800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:85780000-85795800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:85780200-85790400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:85780200-85795800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:85780400-85788200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:85780400-85791600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:85780400-85793200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:85780400-85795800	Weak transcription	Gastric	stomach
26	chr1:85780800-85784000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:85780800-85786400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:85780800-85786400	Weak transcription	Right Ventricle	heart
29	chr1:85780800-85787600	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:85781000-85785600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:85781000-85785800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:85781400-85784200	Enhancers	Fetal Brain Male	brain
33	chr1:85781800-85786000	Weak transcription	Placenta	Placenta
34	chr1:85781800-85786400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:85781800-85792800	Weak transcription	Pancreas	Pancrea
36	chr1:85782200-85790600	Genic enhancers	Muscle Satellite Cultured Cells	--
37	chr1:85782400-85784000	Weak transcription	NH-A	brain
38	chr1:85782400-85784400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:85782400-85785800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:85782400-85795000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:85782600-85784000	Enhancers	HUVEC	blood vessel
42	chr1:85782600-85784600	Enhancers	Fetal Lung	lung
43	chr1:85782600-85785200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:85782800-85784400	Enhancers	Fetal Heart	heart
45	chr1:85782800-85784400	Weak transcription	Right Atrium	heart
46	chr1:85782800-85784800	Strong transcription	HSMM	muscle
47	chr1:85782800-85785600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:85782800-85785800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:85782800-85786400	Weak transcription	Lung	lung
50	chr1:85782800-85794600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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