Variant report

Variant	rs12139160
Chromosome Location	chr1:175950089-175950090
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	chr1:175943129..175946013-chr1:175947654..175950416,2	K562	blood:
2	chr1:175948120..175950951-chr1:175956152..175957990,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10494497	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12119366	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12121832	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs12123116	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12125119	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12125192	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12125328	0.89[CEU][hapmap]
rs12127204	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12127719	0.85[AMR][1000 genomes]
rs12128099	0.90[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12128327	0.90[CEU][hapmap];0.92[AMR][1000 genomes]
rs12129466	0.88[AMR][1000 genomes]
rs12129873	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs12130538	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12132072	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12133268	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12133701	0.92[AMR][1000 genomes]
rs12134392	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs12134984	0.85[AMR][1000 genomes]
rs12135045	0.85[AMR][1000 genomes]
rs12137136	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12140631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12141054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12142010	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12142461	0.90[CEU][hapmap];0.85[AMR][1000 genomes]
rs12144692	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12144806	0.90[CEU][hapmap];0.85[AMR][1000 genomes]
rs12145452	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12145703	0.89[CEU][hapmap]
rs12145778	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs1330863	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs16849475	0.90[CEU][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28770189	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4400573	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs56230548	0.92[AMR][1000 genomes]
rs7349083	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

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	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 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	chr1:175897000-175953000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:175897600-175953200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:175897800-175952400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:175898600-175953200	Weak transcription	Pancreas	Pancrea
5	chr1:175899200-175953200	Weak transcription	Esophagus	oesophagus
6	chr1:175903400-175951400	Weak transcription	K562	blood
7	chr1:175904200-175956200	Weak transcription	Psoas Muscle	Psoas
8	chr1:175904600-175953000	Weak transcription	Right Ventricle	heart
9	chr1:175906400-175952400	Weak transcription	Spleen	Spleen
10	chr1:175906400-175962600	Weak transcription	NH-A	brain
11	chr1:175906800-175952000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:175907400-175950600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:175908000-175959400	Weak transcription	NHEK	skin
14	chr1:175911200-175950400	Weak transcription	Fetal Heart	heart
15	chr1:175916400-175952200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:175917600-175953000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:175921400-175951200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:175922000-175952000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:175924600-175953200	Weak transcription	Gastric	stomach
20	chr1:175924600-175953200	Weak transcription	HepG2	liver
21	chr1:175925000-175951800	Weak transcription	Brain Anterior Caudate	brain
22	chr1:175927000-175951200	Weak transcription	Fetal Brain Male	brain
23	chr1:175930400-175951800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:175930400-175952200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:175930600-175951400	Weak transcription	Fetal Kidney	kidney
26	chr1:175934200-175950400	Weak transcription	GM12878-XiMat	blood
27	chr1:175937400-175951400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:175938000-175951800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:175938200-175951800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:175938400-175950200	Weak transcription	HSMMtube	muscle
31	chr1:175938800-175952200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:175939000-175951400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:175939400-175952200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:175940400-175953800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:175941000-175952600	Weak transcription	Colonic Mucosa	Colon
36	chr1:175941000-175953200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:175941200-175950200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:175941200-175950600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:175941200-175950600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:175941200-175951200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:175941200-175951200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:175941200-175951200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:175941200-175951400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:175941200-175951800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:175941200-175952400	Weak transcription	Left Ventricle	heart
46	chr1:175941200-175952400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:175941200-175952400	Weak transcription	Thymus	Thymus
48	chr1:175941200-175952800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:175941200-175953200	Weak transcription	Lung	lung
50	chr1:175941400-175950400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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