Variant report

Variant	rs16839617
Chromosome Location	chr1:157997676-157997677
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10430456	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11264878	0.81[JPT][hapmap]
rs12021619	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12025305	0.87[AMR][1000 genomes]
rs12037357	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs12039337	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12118340	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12118455	0.91[AMR][1000 genomes]
rs12134949	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12568166	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16839627	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16839630	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16839636	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1972216	0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs1980765	1.00[CEU][hapmap];0.81[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4445460	0.84[GIH][hapmap];0.81[TSI][hapmap]
rs4971179	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4971180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4971183	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs55712021	0.94[EUR][1000 genomes]
rs59269620	0.94[EUR][1000 genomes]
rs6661149	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6665898	0.81[JPT][hapmap]
rs6690504	1.00[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes]
rs6692314	0.91[AMR][1000 genomes]
rs6699860	0.91[AMR][1000 genomes]
rs7527064	0.94[EUR][1000 genomes]
rs7530591	0.94[EUR][1000 genomes]
rs7537784	0.81[GIH][hapmap]
rs7548850	0.81[JPT][hapmap]
rs7555783	1.00[CEU][hapmap];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823720	chr1:157978556-158034017	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:157985200-158006000	Weak transcription	Fetal Thymus	thymus
2	chr1:157989400-158007400	Weak transcription	Gastric	stomach
3	chr1:157991400-158000400	Weak transcription	Fetal Intestine Large	intestine
4	chr1:157991800-158002200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:157991800-158007400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:157992000-157999200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:157992800-158000600	Weak transcription	Thymus	Thymus
8	chr1:157993000-158007400	Weak transcription	HSMMtube	muscle
9	chr1:157993000-158007600	Weak transcription	Esophagus	oesophagus
10	chr1:157993200-158007400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:157993400-157997800	Weak transcription	Hela-S3	cervix
12	chr1:157994200-157998200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:157994400-157999600	Enhancers	A549	lung
14	chr1:157995000-157998000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:157995000-158007800	Weak transcription	Brain Germinal Matrix	brain
16	chr1:157995200-158004200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:157995400-157998000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:157995400-157999400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:157995400-158007600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:157995600-158000000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:157995600-158004400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:157995800-157997800	Weak transcription	Left Ventricle	heart
23	chr1:157995800-158000200	Weak transcription	Fetal Intestine Small	intestine
24	chr1:157995800-158000600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:157995800-158001000	Weak transcription	Fetal Brain Female	brain
26	chr1:157995800-158005600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:157995800-158007400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:157996000-157998000	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr1:157996000-158000400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:157996000-158001000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:157996000-158007400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr1:157996000-158007400	Weak transcription	Lung	lung
33	chr1:157996200-157998000	Weak transcription	NH-A	brain
34	chr1:157996200-158000000	Weak transcription	NHDF-Ad	bronchial
35	chr1:157996200-158000600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:157996200-158000600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:157996200-158006800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:157996200-158007600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:157996200-158007600	Weak transcription	Spleen	Spleen
40	chr1:157996400-157997800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:157996400-157997800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:157996400-157998000	Strong transcription	Fetal Stomach	stomach
43	chr1:157996400-157998000	Strong transcription	NHLF	lung
44	chr1:157996400-157998600	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:157996400-157998600	Weak transcription	Osteobl	bone
46	chr1:157996400-158000400	Weak transcription	Aorta	Aorta
47	chr1:157996400-158001000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:157996400-158005600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:157996400-158007400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr1:157996600-157998000	Genic enhancers	HMEC	breast

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