Variant report

Variant	rs2251768
Chromosome Location	chr1:165738311-165738312
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10800135	1.00[JPT][hapmap]
rs10800153	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800154	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10800155	1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918274	0.94[EUR][1000 genomes]
rs12133745	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403369	1.00[JPT][hapmap]
rs12691499	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12691500	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547725	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs2790049	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790052	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790053	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814463	0.83[ASN][1000 genomes]
rs2814466	1.00[JPT][hapmap]
rs2814471	1.00[CEU][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]
rs28504591	0.80[EUR][1000 genomes]
rs4233408	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4537525	1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603103	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656461	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657471	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4657472	0.83[ASN][1000 genomes]
rs4657474	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4657475	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657476	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657477	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660601	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662839	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668108	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668885	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6696454	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71628393	0.83[ASN][1000 genomes]
rs7518099	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524755	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7528177	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7555523	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv518886	chr1:165714187-165741646	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165737000-165739200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr1:165737000-165739400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:165737200-165738800	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr1:165737200-165739000	Active TSS	H1 Cell Line	embryonic stem cell
5	chr1:165737200-165739000	Active TSS	Fetal Intestine Large	intestine
6	chr1:165737200-165739000	Active TSS	Lung	lung
7	chr1:165737200-165739000	Active TSS	Psoas Muscle	Psoas
8	chr1:165737200-165739200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:165737200-165739200	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:165737200-165739200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:165737200-165739200	Active TSS	Right Atrium	heart
12	chr1:165737200-165739400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr1:165737200-165739400	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr1:165737200-165739600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:165737400-165738400	Active TSS	Fetal Thymus	thymus
16	chr1:165737400-165738600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:165737400-165738600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:165737400-165738600	Active TSS	Fetal Muscle Leg	muscle
19	chr1:165737400-165738600	Active TSS	Placenta	Placenta
20	chr1:165737400-165738800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:165737400-165738800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:165737400-165738800	Active TSS	Brain Germinal Matrix	brain
23	chr1:165737400-165738800	Active TSS	Fetal Intestine Small	intestine
24	chr1:165737400-165738800	Active TSS	Fetal Stomach	stomach
25	chr1:165737400-165739000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:165737400-165739000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:165737400-165739000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:165737400-165739000	Active TSS	Primary T cells fromperipheralblood	blood
29	chr1:165737400-165739000	Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr1:165737400-165739000	Active TSS	Aorta	Aorta
31	chr1:165737400-165739000	Active TSS	Left Ventricle	heart
32	chr1:165737400-165739000	Active TSS	Ovary	ovary
33	chr1:165737400-165739000	Active TSS	Placenta Amnion	Placenta Amnion
34	chr1:165737400-165739000	Bivalent/Poised TSS	HepG2	liver
35	chr1:165737400-165739200	Active TSS	H9 Cell Line	embryonic stem cell
36	chr1:165737400-165739200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:165737400-165739200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:165737400-165739200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:165737400-165739200	Active TSS	Colonic Mucosa	Colon
40	chr1:165737400-165739200	Active TSS	Fetal Muscle Trunk	muscle
41	chr1:165737400-165739200	Active TSS	Right Ventricle	heart
42	chr1:165737400-165739400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:165737400-165739400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:165737400-165739400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:165737400-165739400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:165737400-165739400	Active TSS	A549	lung
47	chr1:165737400-165740200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:165737600-165738400	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr1:165737600-165738400	Active TSS	Stomach Smooth Muscle	stomach
50	chr1:165737600-165738600	Active TSS	Brain Substantia Nigra	brain

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