Variant report

Variant	rs6728627
Chromosome Location	chr2:11382396-11382397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11365381..11369172-chr2:11380510..11384403,4	K562	blood:
2	chr2:11374624..11376647-chr2:11381201..11383592,2	MCF-7	breast:
3	chr2:11381157..11383383-chr2:11504997..11507708,2	MCF-7	breast:
4	chr2:11380163..11381910-chr2:11382008..11384131,2	MCF-7	breast:
5	chr2:11375000..11377998-chr2:11380925..11383500,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230952	Chromatin interaction
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10168084	0.96[CEU][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10169868	0.86[AMR][1000 genomes]
rs10176416	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10187981	0.87[CHB][hapmap]
rs10192483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs10198045	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10495582	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10754958	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10929725	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10929726	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10929727	0.88[CHB][hapmap]
rs10929728	0.87[CHB][hapmap]
rs11674991	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11680818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691429	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11891012	0.84[CHB][hapmap]
rs12465116	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12470004	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12472868	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12475086	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12475627	0.90[ASN][1000 genomes]
rs12478098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12478870	0.81[EUR][1000 genomes]
rs12622447	0.87[CHB][hapmap]
rs12987956	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes]
rs12996399	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs12996712	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13018466	0.80[CEU][hapmap]
rs13022598	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13030319	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13393192	0.82[CEU][hapmap];0.88[CHB][hapmap];0.87[AMR][1000 genomes]
rs13397757	0.82[CEU][hapmap];0.87[AMR][1000 genomes]
rs13404430	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes]
rs13423864	0.88[CHB][hapmap];0.87[AMR][1000 genomes]
rs13424069	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1515219	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546597	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1546598	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17366643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17366657	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17366874	0.96[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17463896	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868585	0.87[CHB][hapmap]
rs1901010	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2011812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2056103	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2060634	0.80[EUR][1000 genomes]
rs2122383	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2176052	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230774	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2290156	0.87[CHB][hapmap]
rs2357997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2358007	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3206843	0.84[AMR][1000 genomes]
rs34193264	0.80[EUR][1000 genomes]
rs34213264	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34586031	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34623763	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34727260	0.81[EUR][1000 genomes]
rs35407012	0.86[EUR][1000 genomes]
rs35432367	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35508648	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35515036	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35563401	0.85[EUR][1000 genomes]
rs36072395	0.87[AMR][1000 genomes]
rs3771106	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4477886	0.96[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4595944	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4669700	0.83[CHB][hapmap]
rs4669702	0.88[CHB][hapmap]
rs4669708	0.87[CHB][hapmap]
rs55641887	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55995833	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56243142	0.84[AMR][1000 genomes]
rs56256182	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57554471	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58263533	0.83[AMR][1000 genomes]
rs62120156	0.86[EUR][1000 genomes]
rs62121446	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121447	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707667	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6711793	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6716447	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6716817	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6736194	0.83[CHB][hapmap]
rs6739310	0.84[CHB][hapmap]
rs6743710	0.83[CHB][hapmap]
rs6753921	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs726843	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs753771	0.80[EUR][1000 genomes]
rs7557723	0.80[EUR][1000 genomes]
rs7560132	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7580593	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7581130	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7589152	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7589629	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7598032	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[AMR][1000 genomes]
rs7600696	0.87[AMR][1000 genomes]
rs8996	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs921321	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs921322	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs978906	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6728627	PQLC3	cis	lung	GTEx
rs6728627	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs6728627	PQLC3	cis	Thyroid	GTEx
rs6728627	ROCK2	cis	multi-tissue	Pritchard

Chromatin state (count:97 , 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	chr2:11333400-11386200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:11339800-11382600	Weak transcription	Esophagus	oesophagus
6	chr2:11341600-11384400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:11352600-11411200	Weak transcription	Thymus	Thymus
8	chr2:11352800-11424000	Weak transcription	HSMMtube	muscle
9	chr2:11354400-11382600	Weak transcription	Ovary	ovary
10	chr2:11354400-11388000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:11354600-11423800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:11360400-11396400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:11360800-11382800	Weak transcription	Spleen	Spleen
14	chr2:11361000-11383800	Weak transcription	Fetal Kidney	kidney
15	chr2:11361000-11397000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:11361000-11397400	Weak transcription	Left Ventricle	heart
17	chr2:11361000-11399200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:11361000-11400200	Weak transcription	Gastric	stomach
19	chr2:11361000-11410800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:11361000-11411200	Weak transcription	Fetal Thymus	thymus
21	chr2:11361000-11416600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr2:11361200-11425600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:11361600-11396800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:11364000-11387000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:11364400-11382400	Weak transcription	Adipose Nuclei	Adipose
26	chr2:11364400-11387600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:11364400-11423800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:11364800-11397400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr2:11365400-11387400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:11365600-11383400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr2:11366000-11382800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:11366000-11391000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:11366400-11396800	Weak transcription	Fetal Muscle Leg	muscle
34	chr2:11366600-11390800	Weak transcription	NHLF	lung
35	chr2:11367600-11387000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:11367600-11387000	Weak transcription	Placenta	Placenta
37	chr2:11367600-11388200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr2:11367800-11387000	Weak transcription	Dnd41	blood
39	chr2:11368200-11387000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:11368400-11394400	Weak transcription	Brain Angular Gyrus	brain
41	chr2:11369600-11382400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:11369600-11388000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:11370400-11394200	Weak transcription	Fetal Lung	lung
44	chr2:11372600-11382600	Weak transcription	Primary T cells from cord blood	blood
45	chr2:11372600-11397200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:11372600-11423800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:11373000-11382400	Weak transcription	Fetal Stomach	stomach
48	chr2:11373400-11387200	Weak transcription	Fetal Intestine Small	intestine
49	chr2:11375400-11390600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:11375600-11387200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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