Variant report

Variant	rs10210600
Chromosome Location	chr2:11454130-11454131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11444757..11447160-chr2:11453898..11455416,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10178332	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10183296	0.81[AMR][1000 genomes]
rs10192593	0.81[YRI][hapmap]
rs10192994	0.93[CEU][hapmap];0.81[AMR][1000 genomes]
rs10194620	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs10203916	1.00[CEU][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10205944	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs10206334	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10208872	0.81[YRI][hapmap]
rs10454126	1.00[CEU][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10754957	0.81[EUR][1000 genomes]
rs10929730	0.95[EUR][1000 genomes]
rs11681822	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11694729	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs11695377	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs12692434	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12692435	0.81[AMR][1000 genomes]
rs12692437	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs12990641	0.85[CEU][hapmap]
rs12992581	0.85[AMR][1000 genomes]
rs12994807	0.87[AMR][1000 genomes]
rs13014721	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13015560	0.81[CEU][hapmap]
rs13017021	0.85[CEU][hapmap]
rs1515224	0.85[EUR][1000 genomes]
rs1562748	1.00[CEU][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1562749	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs1868584	0.93[CEU][hapmap]
rs2044758	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs2060635	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2084577	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2100228	0.86[EUR][1000 genomes]
rs2122384	0.87[AMR][1000 genomes]
rs2167126	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2357996	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs3911110	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4303693	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4669699	0.81[EUR][1000 genomes]
rs4669706	0.84[AMR][1000 genomes]
rs4669709	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4669710	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4669711	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4669712	0.82[AMR][1000 genomes]
rs4669713	1.00[CEU][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes]
rs4669715	0.92[CEU][hapmap]
rs62118012	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6432183	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs6432184	0.93[CEU][hapmap]
rs6432185	0.87[AMR][1000 genomes]
rs6432186	1.00[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6706126	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6710031	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6713273	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6713382	0.81[AMR][1000 genomes]
rs6721445	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6730673	0.81[YRI][hapmap]
rs6733312	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6735090	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6736240	0.87[AMR][1000 genomes]
rs6749456	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6755196	1.00[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6755337	0.81[YRI][hapmap];0.85[AMR][1000 genomes]
rs6760802	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7355446	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7355489	0.81[YRI][hapmap];0.85[AMR][1000 genomes]
rs753770	1.00[CEU][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7558664	0.81[YRI][hapmap]
rs7563928	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7573458	0.92[EUR][1000 genomes]
rs7575837	0.87[AMR][1000 genomes]
rs7593091	1.00[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9287728	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs965665	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs9712182	0.87[AMR][1000 genomes]
rs9808228	0.84[EUR][1000 genomes]
rs9967898	0.84[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10210600	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 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	chr2:11444000-11458600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:11444800-11454600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:11445000-11465200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:11445400-11460200	Weak transcription	Left Ventricle	heart
6	chr2:11447000-11454400	Weak transcription	Fetal Heart	heart
7	chr2:11447000-11456000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:11447000-11459800	Weak transcription	Fetal Kidney	kidney
9	chr2:11447000-11460000	Weak transcription	Ovary	ovary
10	chr2:11447000-11460200	Weak transcription	Fetal Lung	lung
11	chr2:11447200-11454400	Weak transcription	HSMM	muscle
12	chr2:11447200-11454600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:11447200-11456000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:11447200-11466200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:11448000-11454400	Weak transcription	NHDF-Ad	bronchial
16	chr2:11448000-11465800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:11449400-11455400	Enhancers	HepG2	liver
18	chr2:11449600-11458800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:11450400-11454800	Weak transcription	Osteobl	bone
20	chr2:11450400-11455200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr2:11450600-11466600	Weak transcription	NHLF	lung
22	chr2:11451000-11454400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:11451200-11454400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:11451200-11454400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:11451200-11455800	Weak transcription	Fetal Intestine Small	intestine
26	chr2:11451200-11460000	Weak transcription	Adipose Nuclei	Adipose
27	chr2:11451400-11461000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:11451600-11467000	Weak transcription	Primary B cells from cord blood	blood
29	chr2:11451800-11454800	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:11451800-11455800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:11451800-11466000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr2:11452000-11455000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:11452000-11460000	Weak transcription	Psoas Muscle	Psoas
34	chr2:11452000-11466000	Weak transcription	Small Intestine	intestine
35	chr2:11452200-11454200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:11452200-11454600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr2:11452600-11455200	Enhancers	A549	lung
38	chr2:11452800-11454400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:11453400-11454600	Weak transcription	K562	blood
40	chr2:11453400-11456000	Weak transcription	Liver	Liver
41	chr2:11453800-11454600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:11454000-11455000	Enhancers	Pancreatic Islets	Pancreatic Islet

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