Variant report

Variant	rs12476339
Chromosome Location	chr2:127804699-127804700
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11888878	0.96[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11893989	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11902275	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12465042	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12474412	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12477924	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17014784	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17014818	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17014851	0.96[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17040070	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2071268	0.96[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2071270	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768859	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3768860	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3820757	0.87[MEX][hapmap]
rs4662703	0.87[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4663089	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4663090	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55819047	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55999604	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56408880	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60022219	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66507470	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6745677	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67920725	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72481904	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs727095	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72846676	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7570116	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7573824	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs880436	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999422	chr2:127464647-127956543	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1004930	chr2:127477369-127938234	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv459230	chr2:127771006-127844735	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv583032	chr2:127771006-127844735	Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1003730	chr2:127794288-127860830	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1003461	chr2:127794288-127862257	Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv516759	chr2:127796666-127859441	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv1000994	chr2:127797089-127860830	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	esv1825024	chr2:127798138-127864285	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv459241	chr2:127800981-127868435	Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv583033	chr2:127800981-127868435	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv875011	chr2:127800981-127868435	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv875012	chr2:127800981-127895573	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1002673	chr2:127801964-127860830	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv1010577	chr2:127801964-127862257	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv1011224	chr2:127802375-127860830	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv1003887	chr2:127802375-127862257	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1009309	chr2:127802730-127862257	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12476339	AMMECR1L	cis	parietal	SCAN
rs12476339	POLR2D	cis	parietal	SCAN
rs12476339	MYO7B	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127783800-127815600	Weak transcription	Aorta	Aorta
2	chr2:127793200-127805400	Weak transcription	Liver	Liver
3	chr2:127795800-127807600	Weak transcription	Brain Germinal Matrix	brain
4	chr2:127797600-127805200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr2:127797800-127805600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:127798200-127811400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:127799400-127804800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:127799600-127805800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:127799600-127805800	Weak transcription	Gastric	stomach
10	chr2:127799600-127806200	Weak transcription	Brain Angular Gyrus	brain
11	chr2:127800000-127807600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:127800200-127807400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:127801200-127806000	Weak transcription	NHLF	lung
14	chr2:127801600-127807600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:127802000-127818800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:127802200-127813600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:127802400-127816000	Weak transcription	Fetal Brain Male	brain
18	chr2:127802400-127822800	Weak transcription	Fetal Kidney	kidney
19	chr2:127802800-127805400	Weak transcription	Primary T cells from cord blood	blood
20	chr2:127803200-127805400	Weak transcription	Fetal Heart	heart
21	chr2:127803400-127804800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:127803400-127805200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr2:127803600-127805400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:127803600-127805400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:127803600-127805400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:127803600-127805400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:127803600-127805400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:127803600-127805400	Weak transcription	Ovary	ovary
29	chr2:127803600-127805400	Weak transcription	Thymus	Thymus
30	chr2:127803800-127805400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr2:127803800-127805400	Weak transcription	Brain Substantia Nigra	brain
32	chr2:127803800-127806000	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:127803800-127807400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:127803800-127814200	Weak transcription	HSMM	muscle
35	chr2:127804000-127804800	Weak transcription	Adipose Nuclei	Adipose
36	chr2:127804000-127805400	Weak transcription	Lung	lung
37	chr2:127804000-127805600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:127804000-127805800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:127804000-127805800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:127804000-127805800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:127804000-127806000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr2:127804000-127807600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:127804000-127808000	Weak transcription	Right Ventricle	heart
44	chr2:127804000-127810600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:127804000-127813400	Weak transcription	Primary B cells from cord blood	blood
46	chr2:127804000-127814400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:127804200-127804800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:127804200-127805400	Weak transcription	HSMMtube	muscle
49	chr2:127804200-127805800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:127804200-127805800	Weak transcription	Rectal Smooth Muscle	rectum

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