Variant report

Variant	rs6749456
Chromosome Location	chr2:11450625-11450626
allele	G/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	chr2:11444512..11447438-chr2:11450182..11452688,2	K562	blood:
4	chr2:11422735..11425372-chr2:11448792..11450664,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10168440	0.86[AFR][1000 genomes]
rs10178332	0.94[CEU][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10183296	0.82[AMR][1000 genomes]
rs10192593	0.87[GIH][hapmap];0.86[YRI][hapmap]
rs10192994	0.93[CEU][hapmap];0.82[AMR][1000 genomes]
rs10194620	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs10203916	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10205944	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[YRI][hapmap]
rs10206334	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10210600	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10454126	1.00[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10754957	0.81[EUR][1000 genomes]
rs10929730	0.95[EUR][1000 genomes]
rs10929732	0.80[YRI][hapmap]
rs11681822	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11694729	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11695377	1.00[CEU][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes]
rs12692434	1.00[CEU][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12692435	0.84[YRI][hapmap];0.83[AMR][1000 genomes]
rs12692437	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes]
rs12990641	0.87[CEU][hapmap]
rs12992581	0.80[YRI][hapmap];0.87[AMR][1000 genomes]
rs12994807	0.81[YRI][hapmap];0.89[AMR][1000 genomes]
rs13014721	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13015560	0.87[CEU][hapmap]
rs13017021	0.87[CEU][hapmap]
rs1515224	0.85[EUR][1000 genomes]
rs1562748	1.00[CEU][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[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	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2084577	1.00[CEU][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2100228	0.86[EUR][1000 genomes]
rs2122384	0.86[YRI][hapmap];0.89[AMR][1000 genomes]
rs2167126	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2357996	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs3911110	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs4303693	0.94[CEU][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4668720	0.84[YRI][hapmap]
rs4669699	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4669706	0.86[AMR][1000 genomes]
rs4669709	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4669710	1.00[CEU][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4669711	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4669712	0.84[AMR][1000 genomes]
rs4669713	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4669715	0.93[CEU][hapmap]
rs62118012	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6432183	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs6432184	0.93[CEU][hapmap]
rs6432185	0.89[AMR][1000 genomes]
rs6432186	1.00[CEU][hapmap];0.97[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6706126	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6710031	0.93[CEU][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6713273	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6713382	0.82[AMR][1000 genomes]
rs6721445	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6730673	0.87[GIH][hapmap];0.86[YRI][hapmap]
rs6733312	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6735090	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6736240	0.86[YRI][hapmap];0.89[AMR][1000 genomes]
rs6753875	0.81[AMR][1000 genomes]
rs6755196	1.00[CEU][hapmap];0.97[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6755337	0.87[GIH][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs6759490	0.87[GIH][hapmap]
rs6760802	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs7355446	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7355489	0.87[GIH][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs753770	1.00[CEU][hapmap];0.87[GIH][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7558664	0.87[GIH][hapmap];0.86[YRI][hapmap]
rs7563468	0.87[GIH][hapmap];0.89[MKK][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs7563928	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7568064	0.84[YRI][hapmap]
rs7573458	0.92[EUR][1000 genomes]
rs7575837	0.84[YRI][hapmap];0.89[AMR][1000 genomes]
rs7593091	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.92[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	0.89[AMR][1000 genomes]
rs9808228	0.84[EUR][1000 genomes]
rs9967898	0.84[EUR][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	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
4	nsv962059	chr2:11447027-11450757	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:50 , 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	chr2:11447000-11451400	Weak transcription	Small Intestine	intestine
9	chr2:11447000-11454400	Weak transcription	Fetal Heart	heart
10	chr2:11447000-11456000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:11447000-11459800	Weak transcription	Fetal Kidney	kidney
12	chr2:11447000-11460000	Weak transcription	Ovary	ovary
13	chr2:11447000-11460200	Weak transcription	Fetal Lung	lung
14	chr2:11447200-11450800	Weak transcription	A549	lung
15	chr2:11447200-11451000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:11447200-11451000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:11447200-11452600	Weak transcription	Fetal Stomach	stomach
18	chr2:11447200-11454400	Weak transcription	HSMM	muscle
19	chr2:11447200-11454600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:11447200-11456000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:11447200-11466200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr2:11447400-11451400	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:11447800-11450800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr2:11448000-11454400	Weak transcription	NHDF-Ad	bronchial
25	chr2:11448000-11465800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:11448200-11451400	Weak transcription	Psoas Muscle	Psoas
27	chr2:11449400-11452200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:11449400-11455400	Enhancers	HepG2	liver
29	chr2:11449600-11458800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:11449800-11451000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr2:11449800-11451200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:11449800-11451200	Enhancers	Adipose Nuclei	Adipose
33	chr2:11449800-11451200	Enhancers	Fetal Intestine Large	intestine
34	chr2:11449800-11451200	Enhancers	Fetal Intestine Small	intestine
35	chr2:11449800-11451600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:11449800-11452200	Enhancers	Liver	Liver
37	chr2:11450000-11451000	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr2:11450200-11450800	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr2:11450200-11450800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr2:11450200-11451000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:11450200-11451200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr2:11450200-11451600	Weak transcription	Aorta	Aorta
43	chr2:11450400-11451200	Enhancers	HMEC	breast
44	chr2:11450400-11452000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:11450400-11454800	Weak transcription	Osteobl	bone
46	chr2:11450400-11455200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:11450600-11451400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:11450600-11451800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr2:11450600-11451800	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr2:11450600-11466600	Weak transcription	NHLF	lung

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