Variant report

Variant	rs12994807
Chromosome Location	chr2:11451445-11451446
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11449416..11451875-chr2:11454672..11457949,3	K562	blood:
2	chr2:11450066..11451573-chr2:11455094..11457155,2	MCF-7	breast:
3	chr2:11429835..11432089-chr2:11450828..11453411,2	K562	blood:
4	chr2:11444512..11447438-chr2:11450182..11452688,2	K562	blood:

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10169455	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175719	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10183296	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10192593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10192994	1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10194620	1.00[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10203916	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10205944	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs10210600	0.87[AMR][1000 genomes]
rs10929729	0.87[AFR][1000 genomes]
rs10929732	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs11681822	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11694729	0.88[YRI][hapmap]
rs11695377	0.82[YRI][hapmap]
rs12467103	0.80[AMR][1000 genomes]
rs12477052	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12692434	0.89[AMR][1000 genomes]
rs12692435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12992581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002722	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13014721	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1562748	0.82[YRI][hapmap];0.89[AMR][1000 genomes]
rs1868584	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs2060635	0.85[AMR][1000 genomes]
rs2084577	0.82[YRI][hapmap];0.89[AMR][1000 genomes]
rs2122384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230775	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs2290157	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2357995	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3771109	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs4353615	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4668720	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669706	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4669709	0.89[AMR][1000 genomes]
rs4669710	0.82[YRI][hapmap];0.89[AMR][1000 genomes]
rs4669711	0.89[AMR][1000 genomes]
rs4669713	0.82[YRI][hapmap]
rs55714132	0.94[ASN][1000 genomes]
rs57082519	0.94[ASN][1000 genomes]
rs57282107	0.94[ASN][1000 genomes]
rs57339546	0.94[ASN][1000 genomes]
rs57861284	0.94[ASN][1000 genomes]
rs58007526	1.00[ASN][1000 genomes]
rs58275781	0.85[ASN][1000 genomes]
rs59194382	1.00[ASN][1000 genomes]
rs59211791	0.94[ASN][1000 genomes]
rs59266229	0.94[ASN][1000 genomes]
rs59883361	1.00[ASN][1000 genomes]
rs60643530	0.94[ASN][1000 genomes]
rs61575329	1.00[ASN][1000 genomes]
rs62118012	0.89[AMR][1000 genomes]
rs6432184	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs6432185	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6432186	0.82[YRI][hapmap];0.89[AMR][1000 genomes]
rs6706126	0.81[AMR][1000 genomes]
rs6713273	0.88[YRI][hapmap];0.89[AMR][1000 genomes]
rs6713382	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6720821	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6730673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6732258	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6733312	0.81[YRI][hapmap];0.89[AMR][1000 genomes]
rs6735090	0.81[AMR][1000 genomes]
rs6736240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749456	0.81[YRI][hapmap];0.89[AMR][1000 genomes]
rs6753875	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6755196	0.82[YRI][hapmap];0.89[AMR][1000 genomes]
rs6755337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759490	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72785499	0.94[ASN][1000 genomes]
rs7355446	1.00[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7355489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73915106	0.94[ASN][1000 genomes]
rs73915107	0.94[ASN][1000 genomes]
rs73915109	0.94[ASN][1000 genomes]
rs73915134	0.94[ASN][1000 genomes]
rs73915135	0.94[ASN][1000 genomes]
rs73915140	0.94[ASN][1000 genomes]
rs73915144	1.00[ASN][1000 genomes]
rs73915151	1.00[ASN][1000 genomes]
rs73915152	1.00[ASN][1000 genomes]
rs73915154	1.00[ASN][1000 genomes]
rs73915155	1.00[ASN][1000 genomes]
rs73915156	1.00[ASN][1000 genomes]
rs73915158	1.00[ASN][1000 genomes]
rs73915159	1.00[ASN][1000 genomes]
rs73915389	0.84[ASN][1000 genomes]
rs73915390	0.88[ASN][1000 genomes]
rs73915394	0.94[ASN][1000 genomes]
rs73915395	0.94[ASN][1000 genomes]
rs73915396	0.94[ASN][1000 genomes]
rs73917504	0.94[ASN][1000 genomes]
rs73917507	0.94[ASN][1000 genomes]
rs73917508	0.94[ASN][1000 genomes]
rs73917511	0.94[ASN][1000 genomes]
rs753770	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7558664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7563468	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563928	1.00[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7568064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7575837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586803	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs7593091	0.88[YRI][hapmap];0.81[AMR][1000 genomes]
rs7593966	0.80[AMR][1000 genomes]
rs9712182	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526038	chr2:11369078-11489531	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12994807	PQLC3	Cis_1M	lymphoblastoid	RTeQTL
rs12994807	ROCK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11424800-11455200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:11439200-11453000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:11444000-11458600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:11444800-11454600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:11445000-11465200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:11445400-11460200	Weak transcription	Left Ventricle	heart
7	chr2:11446200-11453200	Weak transcription	K562	blood
8	chr2:11447000-11454400	Weak transcription	Fetal Heart	heart
9	chr2:11447000-11456000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:11447000-11459800	Weak transcription	Fetal Kidney	kidney
11	chr2:11447000-11460000	Weak transcription	Ovary	ovary
12	chr2:11447000-11460200	Weak transcription	Fetal Lung	lung
13	chr2:11447200-11452600	Weak transcription	Fetal Stomach	stomach
14	chr2:11447200-11454400	Weak transcription	HSMM	muscle
15	chr2:11447200-11454600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:11447200-11456000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:11447200-11466200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:11448000-11454400	Weak transcription	NHDF-Ad	bronchial
19	chr2:11448000-11465800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:11449400-11452200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:11449400-11455400	Enhancers	HepG2	liver
22	chr2:11449600-11458800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:11449800-11451600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:11449800-11452200	Enhancers	Liver	Liver
25	chr2:11450200-11451600	Weak transcription	Aorta	Aorta
26	chr2:11450400-11452000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:11450400-11454800	Weak transcription	Osteobl	bone
28	chr2:11450400-11455200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:11450600-11451800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr2:11450600-11451800	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr2:11450600-11466600	Weak transcription	NHLF	lung
32	chr2:11450800-11452200	Enhancers	A549	lung
33	chr2:11451000-11451600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:11451000-11452200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr2:11451000-11454400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:11451200-11452000	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr2:11451200-11454400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:11451200-11454400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr2:11451200-11455800	Weak transcription	Fetal Intestine Small	intestine
40	chr2:11451200-11460000	Weak transcription	Adipose Nuclei	Adipose
41	chr2:11451400-11451800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr2:11451400-11451800	Enhancers	Colon Smooth Muscle	Colon
43	chr2:11451400-11452000	Enhancers	Psoas Muscle	Psoas
44	chr2:11451400-11452000	Enhancers	Small Intestine	intestine
45	chr2:11451400-11452200	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr2:11451400-11461000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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