Variant report

Variant	rs1010196
Chromosome Location	chr1:77815566-77815567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:77815529-77816224	PFSK-1	brain:	n/a	n/a
2	RCOR1	chr1:77815541-77816317	K562	blood:	n/a	n/a
3	POLR2A	chr1:77815393-77816180	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77813619..77816574-chr1:78468319..78470340,2	K562	blood:

Variant related genes	Relation type
ENSG00000233099	TF binding region
ENSG00000273338	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10493603	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10747353	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10782646	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11162311	0.87[ASN][1000 genomes]
rs1167196	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1167197	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1167214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12030598	0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12077615	0.87[ASN][1000 genomes]
rs12567557	0.88[JPT][hapmap]
rs12751884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1377738	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1453975	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1453982	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2689680	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs5018314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6603941	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6672375	0.83[LWK][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs7512141	0.87[ASN][1000 genomes]
rs7516300	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7517051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7517698	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[ASN][1000 genomes]
rs7547493	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs7549462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 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	chr1:77789000-77831200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:77795000-77836400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:77801000-77825800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:77803400-77839200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:77809000-77819200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:77812400-77815600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:77813000-77816600	Enhancers	NHDF-Ad	bronchial
8	chr1:77813600-77815600	Weak transcription	Brain Angular Gyrus	brain
9	chr1:77813600-77815800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:77813600-77819800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:77813800-77815800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:77813800-77816000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:77813800-77819400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:77813800-77820600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:77813800-77820600	Weak transcription	NHLF	lung
16	chr1:77813800-77834200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:77814000-77820800	Weak transcription	HSMMtube	muscle
18	chr1:77814200-77815800	Enhancers	K562	blood
19	chr1:77814400-77815800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:77814400-77815800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr1:77814400-77816400	Enhancers	Brain Hippocampus Middle	brain
22	chr1:77814400-77819200	Weak transcription	Primary T cells from cord blood	blood
23	chr1:77814400-77835600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:77814600-77815800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:77814600-77817000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:77814600-77820400	Weak transcription	Osteobl	bone
27	chr1:77814800-77816200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:77814800-77816800	Strong transcription	HSMM	muscle
29	chr1:77815000-77815800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:77815000-77820200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:77815200-77816400	Enhancers	Brain Cingulate Gyrus	brain
32	chr1:77815200-77816400	Enhancers	Brain Substantia Nigra	brain
33	chr1:77815400-77816000	Enhancers	Brain Anterior Caudate	brain

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