Variant report

Variant	rs1253225
Chromosome Location	chr1:77691309-77691310
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:77684564..77687850-chr1:77688271..77692443,7	K562	blood:
2	chr1:77682598..77685827-chr1:77690810..77693587,3	K562	blood:
3	chr1:77690590..77694353-chr1:77694495..77697779,4	K562	blood:

Variant related genes	Relation type
ENSG00000142892	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1028737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10782640	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11162271	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1146673	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1146674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1146675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11806823	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12032956	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12039417	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12093471	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1253217	0.96[ASN][1000 genomes]
rs12562725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1270496	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1314045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs169216	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1779188	0.96[ASN][1000 genomes]
rs199710	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs199711	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs199715	0.90[ASN][1000 genomes]
rs2051127	0.98[ASN][1000 genomes]
rs2069224	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2134351	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4399204	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4443938	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4509622	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4949649	0.82[ASN][1000 genomes]
rs4949766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4949767	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4949771	0.91[ASN][1000 genomes]
rs6603934	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6603936	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6668949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs713232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71592399	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7417698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7522008	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7524151	0.92[ASN][1000 genomes]
rs7525056	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7535408	0.92[ASN][1000 genomes]
rs7538430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7543898	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs940282	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	nsv1006887	chr1:77566348-77698128	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv520629	chr1:77584846-77695854	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv525188	chr1:77655651-77695854	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77685600-77693400	Weak transcription	Pancreas	Pancrea
2	chr1:77685800-77692400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:77685800-77695600	Weak transcription	Left Ventricle	heart
4	chr1:77686000-77691600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:77686000-77692200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:77686000-77692400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:77686000-77694600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:77686000-77694600	Weak transcription	Fetal Kidney	kidney
9	chr1:77686000-77699200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:77686600-77693000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:77686600-77693200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:77686600-77694600	Weak transcription	A549	lung
13	chr1:77686600-77694800	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:77686600-77698200	Weak transcription	Brain Angular Gyrus	brain
15	chr1:77686800-77693000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:77686800-77694600	Weak transcription	Brain Anterior Caudate	brain
17	chr1:77686800-77698000	Weak transcription	HUVEC	blood vessel
18	chr1:77687000-77695200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:77687000-77695200	Weak transcription	NHDF-Ad	bronchial
20	chr1:77687000-77695400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:77688200-77692400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:77688200-77693000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:77688400-77692000	Weak transcription	Aorta	Aorta
24	chr1:77688400-77692200	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:77688400-77692800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:77688400-77693000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:77688400-77694200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:77688400-77697600	Weak transcription	Primary T cells from cord blood	blood
29	chr1:77688600-77692200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:77688800-77692600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:77690800-77692800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:77690800-77693000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:77690800-77695400	Weak transcription	HSMM	muscle

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