Variant report

Variant	rs6730673
Chromosome Location	chr2:11393672-11393673
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10169455	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10175719	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10178332	0.83[AMR][1000 genomes]
rs10183296	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10192593	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10194620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10203916	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs10205944	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs10206334	0.83[AMR][1000 genomes]
rs10210600	0.81[YRI][hapmap]
rs10454126	0.90[YRI][hapmap];0.87[AMR][1000 genomes]
rs10929729	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10929732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11681822	0.94[ASN][1000 genomes]
rs11694729	0.87[GIH][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes]
rs11695377	0.90[YRI][hapmap]
rs12477052	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12692434	0.86[YRI][hapmap]
rs12692435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12692437	0.87[GIH][hapmap];0.83[YRI][hapmap]
rs12992581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12994807	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]
rs13002722	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13014721	0.94[ASN][1000 genomes]
rs1562748	0.90[YRI][hapmap]
rs1868584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2084577	0.90[YRI][hapmap]
rs2122384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2167126	0.83[AMR][1000 genomes]
rs2230775	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2290157	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2357995	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3771109	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3911110	0.89[YRI][hapmap]
rs4303693	0.83[AMR][1000 genomes]
rs4353615	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4668720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4669699	0.81[AMR][1000 genomes]
rs4669701	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4669706	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4669710	0.90[YRI][hapmap]
rs4669713	0.89[YRI][hapmap]
rs55714132	1.00[ASN][1000 genomes]
rs57082519	1.00[ASN][1000 genomes]
rs57282107	1.00[ASN][1000 genomes]
rs57339546	1.00[ASN][1000 genomes]
rs57861284	1.00[ASN][1000 genomes]
rs58007526	0.94[ASN][1000 genomes]
rs58275781	0.91[ASN][1000 genomes]
rs59194382	0.94[ASN][1000 genomes]
rs59211791	1.00[ASN][1000 genomes]
rs59266229	1.00[ASN][1000 genomes]
rs59883361	0.94[ASN][1000 genomes]
rs60643530	1.00[ASN][1000 genomes]
rs61575329	0.94[ASN][1000 genomes]
rs6432184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6432185	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6432186	0.90[YRI][hapmap]
rs6710031	0.83[AMR][1000 genomes]
rs6713273	0.87[GIH][hapmap];0.90[YRI][hapmap]
rs6713382	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6720821	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6721445	0.86[YRI][hapmap];0.85[AMR][1000 genomes]
rs6732258	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6733312	0.86[YRI][hapmap]
rs6736240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6749456	0.87[GIH][hapmap];0.86[YRI][hapmap]
rs6755196	0.90[YRI][hapmap]
rs6755337	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6759490	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760802	0.87[GIH][hapmap]
rs72785499	1.00[ASN][1000 genomes]
rs7355446	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7355489	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73915106	1.00[ASN][1000 genomes]
rs73915107	1.00[ASN][1000 genomes]
rs73915109	1.00[ASN][1000 genomes]
rs73915134	1.00[ASN][1000 genomes]
rs73915135	1.00[ASN][1000 genomes]
rs73915140	1.00[ASN][1000 genomes]
rs73915144	0.94[ASN][1000 genomes]
rs73915151	0.94[ASN][1000 genomes]
rs73915152	0.94[ASN][1000 genomes]
rs73915154	0.94[ASN][1000 genomes]
rs73915155	0.94[ASN][1000 genomes]
rs73915156	0.94[ASN][1000 genomes]
rs73915158	0.94[ASN][1000 genomes]
rs73915159	0.94[ASN][1000 genomes]
rs73915388	0.84[ASN][1000 genomes]
rs73915389	0.90[ASN][1000 genomes]
rs73915390	0.94[ASN][1000 genomes]
rs73915394	1.00[ASN][1000 genomes]
rs73915395	1.00[ASN][1000 genomes]
rs73915396	1.00[ASN][1000 genomes]
rs73917504	1.00[ASN][1000 genomes]
rs73917507	1.00[ASN][1000 genomes]
rs73917508	1.00[ASN][1000 genomes]
rs73917511	1.00[ASN][1000 genomes]
rs753770	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs7558664	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563468	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7563928	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7568064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586803	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7593091	0.87[GIH][hapmap];0.90[YRI][hapmap]
rs7593966	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9712182	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3395022	chr2:11316915-11426380	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1013570	chr2:11321519-11405246	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	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
4	nsv2607	chr2:11381341-11409932	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1827245	chr2:11385834-11442583	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6730673	PQLC3	Cis_1M	lymphoblastoid	RTeQTL
rs6730673	ROCK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11296200-11412600	Weak transcription	Aorta	Aorta
2	chr2:11297600-11394400	Weak transcription	Right Ventricle	heart
3	chr2:11310600-11433000	Weak transcription	Pancreas	Pancrea
4	chr2:11352600-11411200	Weak transcription	Thymus	Thymus
5	chr2:11352800-11424000	Weak transcription	HSMMtube	muscle
6	chr2:11354600-11423800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:11360400-11396400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:11361000-11397000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:11361000-11397400	Weak transcription	Left Ventricle	heart
10	chr2:11361000-11399200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:11361000-11400200	Weak transcription	Gastric	stomach
12	chr2:11361000-11410800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:11361000-11411200	Weak transcription	Fetal Thymus	thymus
14	chr2:11361000-11416600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:11361200-11425600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:11361600-11396800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:11364400-11423800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:11364800-11397400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr2:11366400-11396800	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:11368400-11394400	Weak transcription	Brain Angular Gyrus	brain
21	chr2:11370400-11394200	Weak transcription	Fetal Lung	lung
22	chr2:11372600-11397200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:11372600-11423800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:11376200-11410800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:11376800-11394200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:11376800-11395000	Weak transcription	Fetal Heart	heart
27	chr2:11376800-11399000	Weak transcription	Brain Anterior Caudate	brain
28	chr2:11378800-11428600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:11379800-11397000	Weak transcription	GM12878-XiMat	blood
30	chr2:11380000-11396400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:11380400-11397400	Weak transcription	Right Atrium	heart
32	chr2:11382800-11410200	Weak transcription	Primary B cells from cord blood	blood
33	chr2:11383000-11424000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:11383200-11397200	Weak transcription	Lung	lung
35	chr2:11383200-11397400	Weak transcription	Esophagus	oesophagus
36	chr2:11383200-11409800	Weak transcription	Primary T cells from cord blood	blood
37	chr2:11383400-11410400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr2:11385000-11394000	Weak transcription	Liver	Liver
39	chr2:11385000-11411000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:11386400-11398200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:11387400-11397400	Weak transcription	Dnd41	blood
42	chr2:11387800-11417400	Weak transcription	Placenta	Placenta
43	chr2:11388400-11397000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:11388400-11401000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:11388600-11394200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:11388600-11396400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:11388600-11406400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr2:11388600-11411200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:11388800-11396400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr2:11389000-11396400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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