Variant report

Variant	rs12107256
Chromosome Location	chr3:28308752-28308753
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:28305069..28306910-chr3:28307661..28310186,2	MCF-7	breast:
2	chr3:28291993..28293537-chr3:28308366..28309970,2	K562	blood:
3	chr3:28308378..28310438-chr3:28317239..28319409,2	K562	blood:
4	chr3:28308007..28309776-chr3:28388999..28390940,2	MCF-7	breast:
5	chr3:28308373..28310438-chr3:28316612..28319409,2	K562	blood:
6	chr3:28282261..28284586-chr3:28306765..28309351,2	MCF-7	breast:
7	chr3:28281504..28285453-chr3:28307037..28310728,5	K562	blood:

Variant related genes	Relation type
ENSG00000187118	Chromatin interaction
ENSG00000163512	Chromatin interaction
ENSG00000206559	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs11706332	0.85[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.86[ASN][1000 genomes]
rs11707705	0.85[CHB][hapmap]
rs11708424	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11720107	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs11918050	0.84[CHB][hapmap]
rs11921692	0.84[CHB][hapmap]
rs11921943	0.85[CHB][hapmap]
rs13075840	0.81[CHB][hapmap]
rs13081520	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs13082167	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs13083544	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13085075	0.85[CHB][hapmap]
rs13085245	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13087143	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs13087774	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs13088574	0.85[CHB][hapmap]
rs13090296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13090439	0.85[CHB][hapmap]
rs13092618	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13093242	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095628	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs13095675	0.85[CHB][hapmap]
rs13099152	0.89[ASN][1000 genomes]
rs1457910	0.85[CHB][hapmap]
rs1585211	0.85[CHB][hapmap]
rs1599826	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1606386	0.92[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs1606388	0.92[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs1610238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17021221	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs17021306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021402	0.85[CHB][hapmap]
rs17357206	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs17638742	0.92[CHB][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs17638782	0.89[ASN][1000 genomes]
rs17638991	0.85[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.88[ASN][1000 genomes]
rs17695765	0.85[CHB][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs17695884	0.85[CHB][hapmap]
rs17696025	0.85[CHB][hapmap]
rs17696459	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs1870259	0.84[CHB][hapmap]
rs2016948	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168799	0.85[CHB][hapmap]
rs34017994	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34419916	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34541614	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34574968	0.88[ASN][1000 genomes]
rs34681294	0.86[ASN][1000 genomes]
rs34748842	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35217335	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35232922	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35439056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35460328	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35496780	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35530532	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35565264	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35575798	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35678778	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35736614	0.89[ASN][1000 genomes]
rs35768817	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35845822	0.89[ASN][1000 genomes]
rs35937120	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36105900	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs3762797	0.85[CHB][hapmap]
rs4452283	0.85[CHB][hapmap]
rs4522735	0.89[ASN][1000 genomes]
rs4680909	0.85[CHB][hapmap]
rs4680913	0.85[CHB][hapmap]
rs56946005	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62251105	0.88[ASN][1000 genomes]
rs62251108	0.85[ASN][1000 genomes]
rs62252069	0.89[ASN][1000 genomes]
rs66502736	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66716911	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67023418	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771057	0.85[CHB][hapmap]
rs6771460	0.85[CHB][hapmap]
rs68097246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71087683	0.89[ASN][1000 genomes]
rs7434193	0.83[CHB][hapmap]
rs7635383	0.90[ASN][1000 genomes]
rs7639750	0.85[CHB][hapmap]
rs7641491	0.85[CHB][hapmap]
rs7649498	0.85[CHB][hapmap]
rs7650831	0.84[ASN][1000 genomes]
rs7651883	0.85[CHB][hapmap]
rs952888	0.86[ASN][1000 genomes]
rs9843464	0.85[CHB][hapmap]

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	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28283800-28311400	Weak transcription	Lung	lung
2	chr3:28284000-28309600	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:28284000-28313800	Weak transcription	Ovary	ovary
4	chr3:28284000-28317200	Weak transcription	Gastric	stomach
5	chr3:28284400-28311000	Weak transcription	Fetal Intestine Small	intestine
6	chr3:28284400-28312600	Weak transcription	Fetal Lung	lung
7	chr3:28284400-28321800	Weak transcription	NHLF	lung
8	chr3:28284600-28311200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:28285600-28315400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:28285800-28311000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:28287600-28317000	Weak transcription	Pancreas	Pancrea
12	chr3:28288600-28311200	Weak transcription	Esophagus	oesophagus
13	chr3:28291400-28311200	Weak transcription	Aorta	Aorta
14	chr3:28292800-28311000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:28293600-28311200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:28293800-28309800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:28294000-28309200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:28294200-28314400	Weak transcription	HepG2	liver
19	chr3:28294400-28313800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:28294400-28314200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:28294600-28313800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr3:28294800-28313800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:28294800-28316400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:28295000-28312200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:28295600-28313800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:28295600-28318200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:28298200-28309000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:28300000-28313800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:28300600-28311400	Weak transcription	Brain Anterior Caudate	brain
30	chr3:28301000-28313800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:28301800-28314000	Weak transcription	Brain Angular Gyrus	brain
32	chr3:28302200-28313800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr3:28302600-28309400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:28302600-28313800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:28303000-28314600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:28303000-28316800	Weak transcription	Right Ventricle	heart
37	chr3:28303200-28310000	Weak transcription	Psoas Muscle	Psoas
38	chr3:28303400-28322200	Weak transcription	Small Intestine	intestine
39	chr3:28303600-28313800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:28303600-28340600	Weak transcription	NHEK	skin
41	chr3:28303800-28311200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr3:28303800-28311400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:28303800-28320800	Weak transcription	Placenta	Placenta
44	chr3:28304000-28313000	Weak transcription	Fetal Kidney	kidney
45	chr3:28304000-28314000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:28304200-28313800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:28304200-28332400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr3:28304400-28310800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:28304600-28310200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:28304600-28313200	Weak transcription	Stomach Smooth Muscle	stomach

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