Variant report

Variant	rs2629413
Chromosome Location	chr12:57325577-57325578
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57318495..57320635-chr12:57323936..57326743,2	K562	blood:
2	chr12:57325326..57326887-chr12:57330449..57332916,2	K562	blood:
3	chr12:57302260..57303849-chr12:57325166..57326787,2	MCF-7	breast:
4	chr12:57325090..57327714-chr12:57331602..57333568,3	MCF-7	breast:
5	chr12:57324317..57327083-chr12:57327867..57330911,4	MCF-7	breast:
6	chr12:57324104..57327319-chr12:57348172..57351129,3	MCF-7	breast:
7	chr12:57325236..57327206-chr12:57341575..57344080,3	MCF-7	breast:
8	chr12:57319135..57322195-chr12:57322954..57326796,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000170426	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1072669	0.85[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10876960	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs11172071	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs11172072	0.87[ASN][1000 genomes]
rs11172076	0.82[ASN][1000 genomes]
rs1601405	0.85[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs17119173	0.82[JPT][hapmap]
rs1825514	0.84[ASN][1000 genomes]
rs1872436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782331	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs57926126	0.84[ASN][1000 genomes]
rs58009868	0.84[ASN][1000 genomes]
rs59665366	0.84[ASN][1000 genomes]
rs60101051	0.84[ASN][1000 genomes]
rs719749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs719750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7314055	0.88[JPT][hapmap]
rs7314151	0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7314262	0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7970701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs840160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs840162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs840163	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs844469	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs863459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs864541	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs901069	0.85[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1043846	chr12:57323709-57377509	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57316400-57326800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr12:57321400-57327200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:57321400-57328400	Enhancers	Fetal Thymus	thymus
4	chr12:57322000-57328800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:57323200-57325600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:57324200-57326000	Enhancers	Thymus	Thymus
7	chr12:57324400-57326600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:57324600-57326400	Enhancers	Placenta Amnion	Placenta Amnion
9	chr12:57324800-57328000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr12:57325200-57326000	Enhancers	Primary B cells from cord blood	blood
11	chr12:57325200-57326000	Enhancers	Primary B cells from peripheral blood	blood
12	chr12:57325200-57326000	Enhancers	Dnd41	blood
13	chr12:57325200-57326600	Enhancers	Primary T cells from cord blood	blood
14	chr12:57325200-57327000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:57325200-57327200	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr12:57325200-57327200	Enhancers	NHEK	skin
17	chr12:57325400-57325600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr12:57325400-57325600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr12:57325400-57325600	Enhancers	GM12878-XiMat	blood
20	chr12:57325400-57325800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr12:57325400-57325800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:57325400-57325800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:57325400-57325800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:57325400-57325800	Enhancers	Primary T cells fromperipheralblood	blood
25	chr12:57325400-57325800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr12:57325400-57325800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr12:57325400-57325800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:57325400-57325800	Enhancers	Colon Smooth Muscle	Colon
29	chr12:57325400-57325800	Enhancers	Esophagus	oesophagus
30	chr12:57325400-57325800	Enhancers	Fetal Intestine Large	intestine
31	chr12:57325400-57325800	Enhancers	Right Ventricle	heart
32	chr12:57325400-57325800	Flanking Active TSS	HepG2	liver
33	chr12:57325400-57325800	Enhancers	HSMM	muscle
34	chr12:57325400-57326000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:57325400-57326000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr12:57325400-57326000	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr12:57325400-57326000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:57325400-57326000	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr12:57325400-57326000	Enhancers	Spleen	Spleen
40	chr12:57325400-57326200	Enhancers	H9 Cell Line	embryonic stem cell
41	chr12:57325400-57326200	Enhancers	Fetal Muscle Trunk	muscle
42	chr12:57325400-57326200	Enhancers	Fetal Muscle Leg	muscle
43	chr12:57325400-57326200	Enhancers	Fetal Stomach	stomach
44	chr12:57325400-57326400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr12:57325400-57326400	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr12:57325400-57326400	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr12:57325400-57326400	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr12:57325400-57326400	Enhancers	A549	lung
49	chr12:57325400-57326400	Flanking Active TSS	K562	blood
50	chr12:57325400-57326600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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