Variant report

Variant	rs35493121
Chromosome Location	chr12:57390038-57390039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57144483..57147144-chr12:57389426..57391985,2	MCF-7	breast:
2	chr12:57388586..57390855-chr12:57398700..57400334,2	MCF-7	breast:
3	chr12:57385239..57389108-chr12:57389505..57392552,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166856	Chromatin interaction
ENSG00000166860	Chromatin interaction
ENSG00000025423	Chromatin interaction
ENSG00000198056	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10400412	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10400555	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1044939	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10506347	0.84[GIH][hapmap];0.88[AMR][1000 genomes]
rs10506350	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10506351	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1072670	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11832487	0.95[ASN][1000 genomes]
rs11834851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11834856	0.97[ASN][1000 genomes]
rs11836517	0.97[ASN][1000 genomes]
rs12099695	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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810024	0.90[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12810837	0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12812499	0.96[ASN][1000 genomes]
rs12815538	0.97[ASN][1000 genomes]
rs12818342	0.97[ASN][1000 genomes]
rs12824682	0.97[ASN][1000 genomes]
rs12827039	0.97[ASN][1000 genomes]
rs12827286	0.94[ASN][1000 genomes]
rs1552245	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17119301	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17119327	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17119330	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17119344	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17119352	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17119386	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17119388	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17119390	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17119407	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17119416	0.90[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17119418	0.90[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1843311	0.97[ASN][1000 genomes]
rs1843312	0.97[ASN][1000 genomes]
rs1843313	0.97[ASN][1000 genomes]
rs2035545	0.86[JPT][hapmap]
rs2167306	0.97[ASN][1000 genomes]
rs2270736	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2270737	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2270739	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2279373	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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279743	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2291855	0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2371717	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28589663	0.97[ASN][1000 genomes]
rs2888139	0.96[ASN][1000 genomes]
rs3024974	0.81[CEU][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap]
rs3024975	0.81[CEU][hapmap]
rs34186462	0.97[ASN][1000 genomes]
rs34253098	0.97[ASN][1000 genomes]
rs34359134	0.97[ASN][1000 genomes]
rs34762603	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34969650	0.97[ASN][1000 genomes]
rs35034299	0.97[ASN][1000 genomes]
rs35243318	0.97[ASN][1000 genomes]
rs3782329	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3782330	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3803018	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3894415	0.99[ASN][1000 genomes]
rs4016338	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4039	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4143085	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56128678	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56270558	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56354404	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57056392	0.93[ASN][1000 genomes]
rs57129030	0.97[ASN][1000 genomes]
rs57351760	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs57558853	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58298943	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58389529	0.91[ASN][1000 genomes]
rs60258120	0.96[ASN][1000 genomes]
rs60273384	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60380217	0.97[ASN][1000 genomes]
rs61504157	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67476535	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67771054	0.97[ASN][1000 genomes]
rs67844278	0.99[ASN][1000 genomes]
rs68126184	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs697222	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7135297	0.83[ASN][1000 genomes]
rs7136770	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs71461303	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72482268	0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7298475	0.90[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73114426	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73114428	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73114434	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73114436	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73114437	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73114446	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73114452	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73114457	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73114459	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73114467	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73114468	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73114472	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73116494	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73116501	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73118413	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73131120	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs733629	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs746049	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7487948	0.97[ASN][1000 genomes]
rs754398	0.97[ASN][1000 genomes]
rs755221	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7956166	0.97[ASN][1000 genomes]
rs7961920	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7962771	0.90[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7969312	0.97[ASN][1000 genomes]
rs7972615	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs901068	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57377000-57395200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:57380000-57391400	Weak transcription	Fetal Intestine Large	intestine
3	chr12:57381400-57393800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:57381400-57395400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:57381400-57396400	Weak transcription	HMEC	breast
6	chr12:57381800-57390800	Weak transcription	Dnd41	blood
7	chr12:57381800-57391000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:57381800-57392600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:57381800-57393400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:57381800-57393400	Weak transcription	Pancreas	Pancrea
11	chr12:57381800-57395200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:57381800-57396400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:57381800-57397000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:57382000-57392000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:57382000-57392400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr12:57382600-57393000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr12:57382600-57393200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:57383000-57391400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:57383000-57391800	Weak transcription	A549	lung
20	chr12:57383000-57393600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:57383200-57390800	Weak transcription	HSMM	muscle
22	chr12:57383200-57394400	Weak transcription	Hela-S3	cervix
23	chr12:57383200-57398800	Weak transcription	Fetal Heart	heart
24	chr12:57385000-57390800	Weak transcription	HSMMtube	muscle
25	chr12:57385400-57391800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:57385400-57393600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr12:57385400-57394000	Weak transcription	NH-A	brain
28	chr12:57385400-57395400	Weak transcription	Stomach Mucosa	stomach
29	chr12:57385400-57396000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr12:57385600-57391200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr12:57385600-57391400	Weak transcription	Primary B cells from cord blood	blood
32	chr12:57385600-57391600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr12:57385600-57391800	Weak transcription	Right Atrium	heart
34	chr12:57385600-57392000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr12:57385600-57392800	Weak transcription	NHEK	skin
36	chr12:57385600-57393400	Weak transcription	Left Ventricle	heart
37	chr12:57385600-57393800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr12:57385600-57394200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr12:57385600-57394200	Weak transcription	Ovary	ovary
40	chr12:57385600-57396200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:57385800-57390400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:57385800-57391400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr12:57385800-57391400	Weak transcription	Fetal Thymus	thymus
44	chr12:57385800-57391600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:57385800-57393800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr12:57385800-57394000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr12:57385800-57394000	Weak transcription	Colon Smooth Muscle	Colon
48	chr12:57385800-57395200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:57386000-57391000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr12:57386000-57393000	Weak transcription	Monocytes-CD14+_RO01746	blood

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