Variant report

Variant	rs7546116
Chromosome Location	chr1:77844553-77844554
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77840080..77842951-chr1:77843079..77845956,2	K562	blood:
2	chr1:77838249..77841580-chr1:77844120..77846924,3	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10873935	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs11162326	0.85[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs11162327	0.82[ASN][1000 genomes]
rs11162329	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11162335	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11585455	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs12043793	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12565526	0.85[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs17100509	0.84[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs17100513	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs2198511	0.91[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2602936	0.92[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap]
rs2602937	0.82[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2815307	0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap]
rs28701620	0.82[ASN][1000 genomes]
rs3862893	0.82[ASN][1000 genomes]
rs4949800	0.80[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6603943	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6673059	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6704312	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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77835800-77846400	Weak transcription	Aorta	Aorta
2	chr1:77837200-77845000	Weak transcription	Fetal Stomach	stomach
3	chr1:77837400-77844600	Weak transcription	Brain Angular Gyrus	brain
4	chr1:77837400-77845800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:77837600-77844800	Weak transcription	HSMMtube	muscle
6	chr1:77838600-77845000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:77839000-77854000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:77839800-77844600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:77840000-77844600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:77841000-77844600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:77841600-77844600	Weak transcription	NHLF	lung
12	chr1:77842000-77844800	Weak transcription	NHDF-Ad	bronchial
13	chr1:77842600-77844600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:77842600-77846000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:77842800-77846400	Enhancers	Primary hematopoietic stem cells	blood
16	chr1:77843200-77845000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr1:77843200-77845200	Enhancers	Brain Cingulate Gyrus	brain
18	chr1:77843600-77846600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr1:77843800-77844600	Weak transcription	Brain Substantia Nigra	brain
20	chr1:77844000-77845000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:77844000-77845000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:77844000-77845200	Enhancers	Fetal Intestine Large	intestine
23	chr1:77844200-77844600	Enhancers	Brain Hippocampus Middle	brain
24	chr1:77844200-77845000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:77844200-77845200	Enhancers	Primary T cells from cord blood	blood
26	chr1:77844200-77845200	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr1:77844200-77845600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:77844200-77845800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr1:77844200-77845800	Enhancers	Fetal Intestine Small	intestine
30	chr1:77844400-77844800	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr1:77844400-77844800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr1:77844400-77845000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:77844400-77845000	Enhancers	Brain Anterior Caudate	brain
34	chr1:77844400-77845200	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr1:77844400-77845200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr1:77844400-77845200	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr1:77844400-77845200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr1:77844400-77845400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:77844400-77845400	Enhancers	NH-A	brain
40	chr1:77844400-77845600	Enhancers	HSMM	muscle

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