Variant report

Variant	rs485987
Chromosome Location	chr1:85926881-85926882
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85917225..85920485-chr1:85926526..85929082,3	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12021849	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022443	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12022538	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs12023795	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs12029474	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap]
rs12029684	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs12033170	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap]
rs12033315	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12034206	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs12038279	0.92[EUR][1000 genomes]
rs12041140	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs12043505	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap]
rs12043604	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs12046433	1.00[CEU][hapmap]
rs12047139	0.92[EUR][1000 genomes]
rs12047220	1.00[CHB][hapmap]
rs12049582	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs1851782	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28847138	0.84[EUR][1000 genomes]
rs551786	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61164145	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85915200-85927800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:85917400-85929400	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:85917400-85929400	Weak transcription	Gastric	stomach
4	chr1:85917400-85929800	Weak transcription	Esophagus	oesophagus
5	chr1:85917800-85927200	Weak transcription	NH-A	brain
6	chr1:85917800-85928800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:85919200-85928400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:85919400-85927200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:85919600-85928200	Weak transcription	Fetal Brain Female	brain
10	chr1:85920000-85929600	Weak transcription	Brain Substantia Nigra	brain
11	chr1:85920200-85928000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:85920800-85929000	Weak transcription	HSMMtube	muscle
13	chr1:85922600-85928400	Enhancers	Fetal Intestine Large	intestine
14	chr1:85922600-85929000	Enhancers	Fetal Intestine Small	intestine
15	chr1:85923200-85927000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:85923200-85929800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:85923600-85927000	Enhancers	HepG2	liver
18	chr1:85923600-85928200	Enhancers	Liver	Liver
19	chr1:85924400-85927800	Weak transcription	Pancreas	Pancrea
20	chr1:85924600-85927800	Enhancers	HUVEC	blood vessel
21	chr1:85924800-85927200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:85924800-85928400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:85925000-85927000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:85925000-85928600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:85925000-85928800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr1:85925000-85929200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr1:85925200-85927200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:85925200-85929400	Weak transcription	Aorta	Aorta
29	chr1:85925400-85927000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:85925400-85927000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:85925400-85927200	Enhancers	NHDF-Ad	bronchial
32	chr1:85925400-85928000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:85925400-85928200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:85925400-85929000	Weak transcription	Fetal Stomach	stomach
35	chr1:85925400-85929200	Weak transcription	Adipose Nuclei	Adipose
36	chr1:85925600-85928000	Weak transcription	Fetal Brain Male	brain
37	chr1:85925800-85927200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:85925800-85928200	Weak transcription	Brain Germinal Matrix	brain
39	chr1:85925800-85929200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:85926000-85927000	Weak transcription	Fetal Lung	lung
41	chr1:85926000-85928000	Enhancers	Fetal Kidney	kidney
42	chr1:85926000-85928400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:85926200-85927200	Weak transcription	Stomach Mucosa	stomach
44	chr1:85926200-85927400	Weak transcription	Osteobl	bone
45	chr1:85926200-85927800	Weak transcription	HSMM	muscle
46	chr1:85926200-85928400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:85926400-85927200	Enhancers	NHLF	lung
48	chr1:85926400-85928400	Enhancers	Duodenum Mucosa	Duodenum
49	chr1:85926400-85929000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:85926400-85929200	Enhancers	Rectal Mucosa Donor 29	rectum

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