Variant report

Variant	rs2060635
Chromosome Location	chr2:11469160-11469161
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	chr2:11468962..11471644-chr2:11473176..11474699,2	MCF-7	breast:
2	chr2:11467535..11471011-chr2:11482918..11485202,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10178332	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10203916	0.90[AMR][1000 genomes]
rs10206334	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10210600	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10454126	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10929730	0.91[EUR][1000 genomes]
rs11681822	0.90[AMR][1000 genomes]
rs11694729	0.83[EUR][1000 genomes]
rs12692434	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12692437	0.80[AMR][1000 genomes]
rs12992581	0.83[AMR][1000 genomes]
rs12994807	0.85[AMR][1000 genomes]
rs13014721	0.86[AMR][1000 genomes]
rs1515224	0.82[EUR][1000 genomes]
rs1562748	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1562749	0.80[EUR][1000 genomes]
rs2044758	0.82[EUR][1000 genomes]
rs2084577	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2100228	0.83[EUR][1000 genomes]
rs2122384	0.85[AMR][1000 genomes]
rs2167126	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2357996	0.80[EUR][1000 genomes]
rs3911110	0.80[EUR][1000 genomes]
rs4303693	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4669706	0.82[AMR][1000 genomes]
rs4669709	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4669710	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4669711	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4669712	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4669713	0.80[AMR][1000 genomes]
rs62118012	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6432183	0.80[EUR][1000 genomes]
rs6432185	0.85[AMR][1000 genomes]
rs6432186	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6706126	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6710031	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6713273	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6721445	0.83[EUR][1000 genomes]
rs6733312	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6735090	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6736240	0.85[AMR][1000 genomes]
rs6749456	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6755196	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6755337	0.83[AMR][1000 genomes]
rs6760802	0.82[EUR][1000 genomes]
rs7355446	0.90[AMR][1000 genomes]
rs7355489	0.83[AMR][1000 genomes]
rs753770	0.90[AMR][1000 genomes]
rs7563928	0.90[AMR][1000 genomes]
rs7573458	0.88[EUR][1000 genomes]
rs7575837	0.85[AMR][1000 genomes]
rs7593091	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9287728	0.80[EUR][1000 genomes]
rs965665	0.82[EUR][1000 genomes]
rs9712182	0.85[AMR][1000 genomes]
rs9808228	0.80[EUR][1000 genomes]
rs9967898	0.80[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2060635	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs2060635	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11454400-11469800	Weak transcription	Fetal Brain Male	brain
2	chr2:11455000-11469200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:11456000-11469400	Weak transcription	HSMM	muscle
4	chr2:11457200-11476400	Weak transcription	Fetal Intestine Small	intestine
5	chr2:11457400-11469800	Weak transcription	Hela-S3	cervix
6	chr2:11459800-11469400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:11460600-11469400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:11460800-11469800	Weak transcription	Fetal Lung	lung
9	chr2:11461000-11476400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:11461200-11469400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:11464400-11475200	Weak transcription	Aorta	Aorta
12	chr2:11466200-11469400	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:11466800-11469600	Weak transcription	Liver	Liver
14	chr2:11467000-11470200	Weak transcription	NHLF	lung
15	chr2:11467000-11480200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:11467400-11470000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:11467400-11470400	Weak transcription	K562	blood
18	chr2:11467400-11472600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:11467400-11481200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:11467600-11469400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:11467600-11469600	Weak transcription	A549	lung
22	chr2:11467600-11469600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr2:11467600-11470400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr2:11467600-11471400	Weak transcription	Brain Angular Gyrus	brain
25	chr2:11467600-11472000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:11467600-11481600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:11467800-11469400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:11467800-11470000	Weak transcription	GM12878-XiMat	blood
29	chr2:11467800-11470400	Weak transcription	Right Atrium	heart
30	chr2:11467800-11470800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:11467800-11470800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:11467800-11471400	Weak transcription	Right Ventricle	heart
33	chr2:11467800-11471400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:11467800-11473400	Weak transcription	Adipose Nuclei	Adipose
35	chr2:11467800-11480200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:11468000-11469800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:11468000-11470400	Weak transcription	Ovary	ovary
38	chr2:11468000-11476400	Weak transcription	Psoas Muscle	Psoas
39	chr2:11468200-11469200	Weak transcription	NHDF-Ad	bronchial
40	chr2:11468200-11470600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:11468400-11481200	Weak transcription	HUVEC	blood vessel
42	chr2:11469000-11469400	Weak transcription	HepG2	liver

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