Variant report

Variant	rs12239491
Chromosome Location	chr1:168803522-168803523
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	chr1:168803305..168804821-chr1:168806997..168808555,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12405834	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12405968	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12407010	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12407753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410966	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322500	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13375532	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59682281	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61567478	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74123028	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74123029	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74123030	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74123031	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74123035	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74123036	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7525887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7547710	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548313	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs7548404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs857646	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv831847	chr1:168669877-168850129	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv464250	chr1:168772393-168826032	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv548145	chr1:168772393-168826032	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3364789	chr1:168803428-168805376	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168799200-168804000	Enhancers	Fetal Intestine Small	intestine
2	chr1:168799200-168804000	Enhancers	Stomach Mucosa	stomach
3	chr1:168800200-168804000	Enhancers	Fetal Intestine Large	intestine
4	chr1:168801600-168803800	Enhancers	Left Ventricle	heart
5	chr1:168801600-168804200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr1:168801800-168803800	Enhancers	Right Ventricle	heart
7	chr1:168801800-168806000	Enhancers	Fetal Heart	heart
8	chr1:168802600-168803600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr1:168802600-168803800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr1:168802600-168803800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr1:168802600-168803800	Enhancers	Fetal Muscle Leg	muscle
12	chr1:168802600-168803800	Enhancers	Pancreas	Pancrea
13	chr1:168802600-168804000	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr1:168802600-168804000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:168802600-168804000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:168802800-168803600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr1:168802800-168803800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:168802800-168803800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr1:168802800-168803800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:168802800-168803800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:168802800-168803800	Enhancers	Colonic Mucosa	Colon
22	chr1:168802800-168803800	Enhancers	Fetal Thymus	thymus
23	chr1:168802800-168803800	Enhancers	Small Intestine	intestine
24	chr1:168802800-168803800	Enhancers	Dnd41	blood
25	chr1:168802800-168803800	Flanking Active TSS	HepG2	liver
26	chr1:168802800-168804000	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr1:168802800-168804000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr1:168802800-168804000	Enhancers	Fetal Lung	lung
29	chr1:168802800-168805800	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr1:168803000-168803800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:168803000-168803800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr1:168803000-168803800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:168803000-168803800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:168803000-168803800	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr1:168803000-168803800	Enhancers	Fetal Stomach	stomach
36	chr1:168803000-168803800	Enhancers	Right Atrium	heart
37	chr1:168803000-168803800	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr1:168803000-168804000	Enhancers	Ovary	ovary
39	chr1:168803000-168804000	Enhancers	A549	lung
40	chr1:168803200-168803600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:168803200-168803800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:168803200-168803800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:168803200-168803800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr1:168803200-168804000	Enhancers	Primary T cells from cord blood	blood
45	chr1:168803200-168804000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr1:168803200-168804000	Enhancers	Liver	Liver
47	chr1:168803200-168804000	Enhancers	Fetal Kidney	kidney

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