Variant report

Variant	rs684569
Chromosome Location	chr1:85904009-85904010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10489511	1.00[YRI][hapmap]
rs10747319	1.00[YRI][hapmap]
rs11161608	1.00[YRI][hapmap]
rs1342324	0.89[AFR][1000 genomes]
rs233048	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs233049	0.89[AFR][1000 genomes]
rs233056	0.84[AFR][1000 genomes]
rs233065	0.84[AFR][1000 genomes]
rs233073	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs233076	0.84[AFR][1000 genomes]
rs233082	0.89[AFR][1000 genomes]
rs233089	0.89[AFR][1000 genomes]
rs233092	0.89[AFR][1000 genomes]
rs233096	0.89[AFR][1000 genomes]
rs414484	0.84[AFR][1000 genomes]
rs641864	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6685360	1.00[AFR][1000 genomes]
rs7526667	1.00[YRI][hapmap]
rs7552422	1.00[YRI][hapmap]

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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85874400-85904200	Weak transcription	NH-A	brain
2	chr1:85886400-85914200	Weak transcription	HSMMtube	muscle
3	chr1:85892200-85906200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:85893800-85906200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:85893800-85916800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:85894600-85904200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:85897000-85904200	Weak transcription	Fetal Intestine Large	intestine
8	chr1:85897800-85904200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:85897800-85904800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:85899200-85914800	Weak transcription	Esophagus	oesophagus
11	chr1:85901400-85923000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:85902000-85904200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:85902200-85904400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr1:85902400-85905200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr1:85902400-85905200	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr1:85902400-85905400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:85902400-85906200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:85902600-85912200	Weak transcription	Pancreas	Pancrea
19	chr1:85902800-85904400	Enhancers	H9 Cell Line	embryonic stem cell
20	chr1:85902800-85905400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr1:85903000-85904200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:85903000-85906000	Weak transcription	Ovary	ovary
23	chr1:85903000-85906800	Weak transcription	Lung	lung
24	chr1:85903400-85904200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:85903400-85904200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:85903400-85907000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:85903600-85904400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr1:85903600-85904600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:85903600-85904800	Genic enhancers	HSMM	muscle
30	chr1:85903600-85905000	Enhancers	Liver	Liver
31	chr1:85903600-85905200	Enhancers	Fetal Kidney	kidney
32	chr1:85903600-85906600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:85903600-85906800	Enhancers	Adipose Nuclei	Adipose
34	chr1:85903600-85907000	Enhancers	HepG2	liver
35	chr1:85903600-85907200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr1:85903600-85907200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:85903600-85907600	Enhancers	NHDF-Ad	bronchial
38	chr1:85903800-85904400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:85903800-85904600	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr1:85903800-85904600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr1:85903800-85906800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:85903800-85906800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:85903800-85907200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:85903800-85907400	Enhancers	HUVEC	blood vessel
45	chr1:85903800-85907400	Enhancers	NHLF	lung
46	chr1:85903800-85907400	Enhancers	Osteobl	bone
47	chr1:85904000-85904400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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