Variant report

Variant	rs12468175
Chromosome Location	chr2:20830590-20830591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20633992..20655025-chr2:20829429..20854651,127	MCF-7	breast:
2	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
3	chr2:20824547..20826774-chr2:20828873..20830778,2	K562	blood:

Variant related genes	Relation type
ENSG00000228950	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000118960	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10186292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186814	0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187254	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191266	0.90[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10199441	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10432583	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1047169	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11096680	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11687806	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476211	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12710742	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12998196	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs13022516	0.84[ASN][1000 genomes]
rs1344836	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs1529896	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1865678	1.00[ASW][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2033639	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033640	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305457	0.86[CEU][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3732151	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796064	0.91[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4402715	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666317	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4666318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666438	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4666439	0.88[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4666445	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4666446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666449	0.90[CHB][hapmap]
rs60569709	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62122089	0.85[ASN][1000 genomes]
rs6737130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7423811	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875672	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1008473	chr2:20811359-20879186	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv535599	chr2:20811359-20879186	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv517472	chr2:20814583-20855176	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv873725	chr2:20814583-20855176	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
6	nsv527901	chr2:20818458-20876386	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
7	nsv999269	chr2:20824833-20869372	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
8	nsv873726	chr2:20829962-20876260	Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20815000-20831800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:20815000-20847600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:20817400-20831400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:20817400-20835200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:20817400-20847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:20817600-20832200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:20817600-20850000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:20817800-20833800	Weak transcription	Fetal Thymus	thymus
9	chr2:20818200-20835000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:20818200-20835000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:20818400-20831800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:20818800-20833600	Weak transcription	A549	lung
13	chr2:20818800-20842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:20819000-20847400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:20819400-20834200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:20819400-20847800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr2:20819800-20834200	Weak transcription	Osteobl	bone
18	chr2:20820600-20849400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:20820800-20849600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:20821400-20831800	Weak transcription	NHEK	skin
21	chr2:20822000-20832600	Weak transcription	Hela-S3	cervix
22	chr2:20823000-20833600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:20823000-20833600	Weak transcription	HSMMtube	muscle
24	chr2:20823000-20842000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:20823200-20831800	Weak transcription	HMEC	breast
26	chr2:20823400-20834200	Weak transcription	Small Intestine	intestine
27	chr2:20824000-20833600	Strong transcription	Fetal Intestine Small	intestine
28	chr2:20824600-20833600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:20824600-20834000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:20824600-20834200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:20824600-20835000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:20824600-20837400	Weak transcription	Thymus	Thymus
33	chr2:20824600-20837800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr2:20824600-20839000	Weak transcription	Dnd41	blood
35	chr2:20824800-20837400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:20825000-20831400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:20825200-20832800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:20825200-20833600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:20825400-20832800	Weak transcription	Colonic Mucosa	Colon
40	chr2:20825400-20841000	Weak transcription	Primary B cells from cord blood	blood
41	chr2:20825600-20833000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:20825600-20833800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr2:20825600-20836600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr2:20825800-20831400	Weak transcription	HepG2	liver
45	chr2:20826200-20832800	Strong transcription	Spleen	Spleen
46	chr2:20826400-20833000	Weak transcription	Stomach Mucosa	stomach
47	chr2:20826600-20832800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr2:20827000-20832400	Strong transcription	Primary B cells from peripheral blood	blood
49	chr2:20827000-20833400	Weak transcription	Pancreas	Pancrea
50	chr2:20827000-20834200	Weak transcription	NHLF	lung

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