Variant report

Variant	rs2173086
Chromosome Location	chr12:62878970-62878971
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:62860603..62862408-chr12:62877064..62881508,4	MCF-7	breast:
2	chr12:62859326..62863326-chr12:62876630..62881311,5	K562	blood:

Variant related genes	Relation type
ENSG00000061987	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10161203	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10459257	0.87[GIH][hapmap]
rs1056340	0.84[GIH][hapmap]
rs10784301	0.81[GIH][hapmap];0.86[MEX][hapmap]
rs10877854	0.81[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap]
rs10877858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877861	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1157629	0.84[GIH][hapmap]
rs1603823	0.81[CHD][hapmap];0.81[GIH][hapmap];0.82[MEX][hapmap]
rs17098060	0.84[JPT][hapmap]
rs1874881	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133304	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3858677	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4763023	0.81[CHD][hapmap];0.81[GIH][hapmap];0.82[MEX][hapmap]
rs4763167	1.00[ASW][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.87[ASN][1000 genomes]
rs4763171	0.81[CHD][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap]
rs61919481	0.86[ASN][1000 genomes]
rs6581450	0.81[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs6581451	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7309087	0.87[ASN][1000 genomes]
rs7953380	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[ASN][1000 genomes]
rs7965248	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970112	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv899158	chr12:62783967-62937259	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62861800-62879800	Weak transcription	HSMMtube	muscle
2	chr12:62861800-62902200	Weak transcription	Fetal Kidney	kidney
3	chr12:62862800-62895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:62863200-62879400	Weak transcription	Thymus	Thymus
5	chr12:62863200-62881400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:62863200-62895200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:62863200-62896800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:62863200-62901800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:62863200-62937400	Weak transcription	Pancreas	Pancrea
10	chr12:62863400-62895400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:62863400-62902000	Weak transcription	HUVEC	blood vessel
12	chr12:62863400-62911000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:62863600-62892600	Weak transcription	NH-A	brain
14	chr12:62863600-62926400	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:62864000-62894400	Weak transcription	Spleen	Spleen
16	chr12:62864000-62899200	Weak transcription	Brain Germinal Matrix	brain
17	chr12:62864000-62901600	Weak transcription	Lung	lung
18	chr12:62864000-62901600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:62864000-62906200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:62866000-62892000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:62866000-62895400	Weak transcription	Left Ventricle	heart
22	chr12:62866200-62887400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:62866200-62897000	Weak transcription	K562	blood
24	chr12:62866200-62899200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:62866200-62906200	Weak transcription	Aorta	Aorta
26	chr12:62866600-62896000	Weak transcription	Fetal Brain Female	brain
27	chr12:62866600-62906200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:62866600-62912400	Weak transcription	NHLF	lung
29	chr12:62866600-62953200	Weak transcription	Psoas Muscle	Psoas
30	chr12:62866800-62883800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:62866800-62888400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:62867000-62890200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:62867200-62898600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:62869000-62892000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:62869000-62904400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:62871000-62910800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr12:62871200-62895200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:62871800-62891200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:62871800-62891400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:62871800-62891400	Weak transcription	Fetal Intestine Small	intestine
41	chr12:62871800-62892400	Weak transcription	Osteobl	bone
42	chr12:62871800-62895200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr12:62871800-62895400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:62871800-62897200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:62871800-62926200	Weak transcription	Fetal Brain Male	brain
46	chr12:62872000-62879200	Weak transcription	HepG2	liver
47	chr12:62872000-62887800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:62872000-62888800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr12:62872000-62894200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr12:62872200-62891200	Weak transcription	Placenta	Placenta

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