Variant report

Variant	rs12030598
Chromosome Location	chr1:77820127-77820128
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	chr1:77813535..77817247-chr1:77819129..77821661,3	K562	blood:

Variant related genes	Relation type
ENSG00000233099	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1010196	0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10493603	0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs10747353	0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs10782646	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs1167214	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs12567557	0.82[JPT][hapmap]
rs12751884	0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs1377738	0.83[ASN][1000 genomes]
rs1453975	0.81[ASN][1000 genomes]
rs17369082	1.00[YRI][hapmap]
rs2689680	0.94[JPT][hapmap]
rs3844165	1.00[ASW][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs5018314	0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs7517051	0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs7517698	0.85[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap]
rs7547493	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7549462	0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]

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:28 , 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	chr1:77813800-77820600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:77813800-77820600	Weak transcription	NHLF	lung
7	chr1:77813800-77834200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:77814000-77820800	Weak transcription	HSMMtube	muscle
9	chr1:77814400-77835600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:77814600-77820400	Weak transcription	Osteobl	bone
11	chr1:77815000-77820200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:77816000-77824000	Weak transcription	Brain Anterior Caudate	brain
13	chr1:77816200-77825800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:77816800-77820400	Weak transcription	HSMM	muscle
15	chr1:77817400-77834200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:77819200-77820400	Enhancers	Primary T cells from cord blood	blood
17	chr1:77819200-77821400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:77819400-77820600	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr1:77819400-77821000	Enhancers	Brain Hippocampus Middle	brain
20	chr1:77819600-77820200	Enhancers	Fetal Brain Male	brain
21	chr1:77819600-77820400	Enhancers	Brain Angular Gyrus	brain
22	chr1:77819600-77821000	Enhancers	Brain Cingulate Gyrus	brain
23	chr1:77819800-77820400	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr1:77819800-77822200	Weak transcription	Brain Substantia Nigra	brain
25	chr1:77819800-77826800	Weak transcription	NHDF-Ad	bronchial
26	chr1:77819800-77835600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:77820000-77820400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:77820000-77820600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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