Variant report

Variant	rs12987194
Chromosome Location	chr2:189185726-189185727
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	chr2:189153673..189157464-chr2:189183823..189187433,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144366	Chromatin interaction

Extended variants
information (count: 159 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs10167709	0.88[ASN][1000 genomes]
rs10169317	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10170220	0.81[CEU][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs10174928	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10179504	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10180687	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180956	0.81[EUR][1000 genomes]
rs10182377	0.83[ASN][1000 genomes]
rs10185828	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10189376	0.94[ASN][1000 genomes]
rs10192374	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10198025	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10199112	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10199264	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10202605	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10204674	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10206167	0.83[ASN][1000 genomes]
rs10206696	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10209733	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10210696	0.82[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10211189	0.81[CEU][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs10804020	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs10931355	0.81[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs10931358	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1125099	0.93[CHD][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap]
rs11682085	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12151691	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12329399	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12693491	0.81[MEX][hapmap]
rs12693493	0.81[MEX][hapmap]
rs12693497	0.81[MEX][hapmap]
rs12693498	0.88[ASN][1000 genomes]
rs12990374	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13008931	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs13014693	0.84[ASN][1000 genomes]
rs13384413	0.86[ASN][1000 genomes]
rs13387350	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13388723	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13388746	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13389155	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13389879	0.88[ASN][1000 genomes]
rs13394421	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13397237	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13397399	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13403228	0.81[MEX][hapmap]
rs13412312	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13415123	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13420369	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13422836	0.83[ASN][1000 genomes]
rs13423891	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13424536	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13426709	0.83[ASN][1000 genomes]
rs13427070	0.82[ASN][1000 genomes]
rs13429075	0.81[MEX][hapmap]
rs2004888	0.81[MEX][hapmap]
rs28564315	0.88[EUR][1000 genomes]
rs34189381	0.83[ASN][1000 genomes]
rs34209722	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34253555	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34353529	0.81[MEX][hapmap]
rs34737832	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35954758	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35964306	0.84[ASN][1000 genomes]
rs36070354	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs36174757	0.84[EUR][1000 genomes]
rs3889818	0.86[EUR][1000 genomes]
rs3890574	1.00[CEU][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs4128404	0.81[MEX][hapmap]
rs4261684	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4274570	0.94[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4340469	1.00[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4349309	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4361092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4381754	0.81[CEU][hapmap];0.93[JPT][hapmap]
rs4398237	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4426503	0.81[ASN][1000 genomes]
rs4430902	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];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4433962	0.81[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4453654	0.80[CHD][hapmap]
rs4458180	1.00[CEU][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4476318	0.81[EUR][1000 genomes]
rs4513258	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4516391	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs4522565	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4591312	0.81[ASN][1000 genomes]
rs4592814	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4610010	0.81[ASN][1000 genomes]
rs4640356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666758	0.89[ASW][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.94[ASN][1000 genomes]
rs4666759	0.80[ASN][1000 genomes]
rs4667215	0.81[ASN][1000 genomes]
rs4667226	0.81[CEU][hapmap]
rs4667227	1.00[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs4992744	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55693630	0.81[EUR][1000 genomes]
rs56072532	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58966470	0.83[ASN][1000 genomes]
rs58978246	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59106803	0.80[ASN][1000 genomes]
rs59206116	0.87[EUR][1000 genomes]
rs60796263	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62183206	0.80[ASN][1000 genomes]
rs6434269	0.81[JPT][hapmap]
rs6434273	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6434280	0.91[EUR][1000 genomes]
rs66923332	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs66971459	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6704814	1.00[CEU][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs6706666	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs67086516	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67092191	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6712056	0.81[ASN][1000 genomes]
rs6718697	0.86[YRI][hapmap]
rs6718999	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67240894	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6727850	1.00[CEU][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes]
rs6729182	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6732963	0.89[EUR][1000 genomes]
rs6737728	0.83[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs6739162	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6743120	1.00[CEU][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes]
rs6743636	0.81[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs6744629	0.81[JPT][hapmap]
rs6756220	1.00[CEU][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes]
rs6759539	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6759766	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6761769	1.00[CEU][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes]
rs67790470	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67798410	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67919447	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72907672	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7420700	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7425596	0.81[ASN][1000 genomes]
rs7559554	0.80[CHD][hapmap]
rs7561448	0.90[EUR][1000 genomes]
rs7566619	0.88[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs7571197	0.81[MEX][hapmap]
rs7574262	0.88[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs7579610	0.83[ASN][1000 genomes]
rs7582137	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7585703	0.81[JPT][hapmap]
rs7586390	0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs7593215	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7593546	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7595327	0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs7595377	0.94[CEU][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7606178	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7607063	0.88[ASN][1000 genomes]
rs9288157	0.86[ASN][1000 genomes]
rs9808523	0.81[MEX][hapmap]
rs9808557	0.93[CEU][hapmap];0.87[EUR][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	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv431890	chr2:189175905-189202876	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1010330	chr2:189182307-189265614	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv584053	chr2:189184422-189245515	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv999135	chr2:189184937-189265614	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv275130	chr2:189185131-189188518	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv584054	chr2:189185726-189233419	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12987194	COL3A1	cis	parietal	SCAN
rs12987194	MYO1B	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189169400-189187200	Weak transcription	NHLF	lung
2	chr2:189178400-189191400	Weak transcription	Fetal Lung	lung
3	chr2:189179400-189187600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:189179800-189187400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:189180400-189187400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:189181800-189187400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:189182000-189187000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:189182000-189191400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:189182000-189192200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:189182600-189185800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr2:189183000-189187200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:189183000-189196000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr2:189183400-189187000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:189183400-189187000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:189183400-189187000	Weak transcription	Stomach Mucosa	stomach
16	chr2:189183400-189187400	Weak transcription	NH-A	brain
17	chr2:189183400-189197200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:189183400-189198400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:189183600-189187000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:189183600-189187000	Weak transcription	NHDF-Ad	bronchial
21	chr2:189183600-189205000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:189183600-189205400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:189183800-189187000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:189183800-189187000	Weak transcription	Osteobl	bone
25	chr2:189183800-189187200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:189183800-189187400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:189183800-189187400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:189183800-189187400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:189183800-189187400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:189183800-189187400	Weak transcription	Aorta	Aorta
31	chr2:189183800-189198600	Weak transcription	Ovary	ovary
32	chr2:189185000-189186400	Weak transcription	A549	lung
33	chr2:189185000-189186800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:189185000-189186800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr2:189185000-189187200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:189185000-189191600	Weak transcription	Placenta	Placenta
37	chr2:189185200-189187000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:189185400-189187000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:189185400-189187200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:189185400-189189200	Enhancers	HUVEC	blood vessel

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