Variant report

Variant	rs157407
Chromosome Location	chr17:19714206-19714207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs118943	0.93[GIH][hapmap]
rs123082	0.99[ASN][1000 genomes]
rs150122	0.93[GIH][hapmap]
rs157387	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.99[ASN][1000 genomes]
rs157391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs157392	0.99[ASN][1000 genomes]
rs157393	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs157395	0.93[GIH][hapmap]
rs157396	0.93[GIH][hapmap]
rs157397	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs157402	0.89[GIH][hapmap]
rs157406	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs169513	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs172186	0.89[GIH][hapmap]
rs188138	0.93[GIH][hapmap]
rs192511	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs205090	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[ASN][1000 genomes]
rs205093	0.93[GIH][hapmap]
rs205095	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs205096	0.93[GIH][hapmap]
rs205097	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs205106	1.00[ASN][1000 genomes]
rs205107	0.93[GIH][hapmap]
rs205108	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.97[ASN][1000 genomes]
rs205109	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs205110	0.93[GIH][hapmap]
rs205111	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.97[ASN][1000 genomes]
rs281328	0.96[ASN][1000 genomes]
rs281329	0.93[ASN][1000 genomes]
rs281331	0.97[ASN][1000 genomes]
rs281332	0.93[GIH][hapmap]
rs281334	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs281342	0.93[GIH][hapmap]
rs281344	0.95[ASN][1000 genomes]
rs281345	0.96[ASN][1000 genomes]
rs281346	0.93[GIH][hapmap]
rs281347	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs281349	0.97[ASN][1000 genomes]
rs281351	0.93[GIH][hapmap]
rs281353	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.97[ASN][1000 genomes]
rs281356	0.97[ASN][1000 genomes]
rs3098902	1.00[ASN][1000 genomes]
rs3098906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3098908	0.96[ASN][1000 genomes]
rs3098909	0.94[ASN][1000 genomes]
rs3098910	0.86[ASN][1000 genomes]
rs3101810	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs3101814	0.82[JPT][hapmap];1.00[ASN][1000 genomes]
rs383948	0.87[ASN][1000 genomes]
rs394008	0.87[ASN][1000 genomes]
rs395130	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs445958	0.99[ASN][1000 genomes]
rs6587203	0.89[GIH][hapmap]
rs917519	0.86[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv482398	chr17:19673458-19808039	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1057469	chr17:19696714-19787062	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19673800-19769800	Weak transcription	NH-A	brain
2	chr17:19680000-19726800	Weak transcription	NHLF	lung
3	chr17:19700200-19722600	Weak transcription	Esophagus	oesophagus
4	chr17:19700200-19727000	Weak transcription	Right Ventricle	heart
5	chr17:19700400-19745200	Weak transcription	Stomach Mucosa	stomach
6	chr17:19700400-19768400	Weak transcription	Fetal Heart	heart
7	chr17:19700800-19769800	Weak transcription	HSMMtube	muscle
8	chr17:19701000-19726600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr17:19701000-19726800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr17:19701000-19727000	Weak transcription	Thymus	Thymus
11	chr17:19701000-19728000	Weak transcription	HUVEC	blood vessel
12	chr17:19701000-19728200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr17:19701000-19732400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr17:19701000-19743200	Weak transcription	Gastric	stomach
15	chr17:19701000-19743400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr17:19701000-19748600	Weak transcription	Spleen	Spleen
17	chr17:19701000-19753400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr17:19701000-19766200	Weak transcription	Primary B cells from cord blood	blood
19	chr17:19701000-19770000	Weak transcription	Colonic Mucosa	Colon
20	chr17:19701200-19758400	Weak transcription	Small Intestine	intestine
21	chr17:19701400-19726800	Weak transcription	HSMM	muscle
22	chr17:19701800-19742800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr17:19703800-19727000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr17:19703800-19769800	Weak transcription	Psoas Muscle	Psoas
25	chr17:19704200-19722800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr17:19704200-19726000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr17:19704400-19726400	Weak transcription	Fetal Thymus	thymus
28	chr17:19704400-19754800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr17:19704400-19770000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr17:19704600-19721800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr17:19705200-19717600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr17:19705200-19721000	Weak transcription	Left Ventricle	heart
33	chr17:19705200-19722800	Weak transcription	Fetal Intestine Small	intestine
34	chr17:19705200-19722800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr17:19705200-19726400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr17:19705200-19726600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr17:19705200-19733200	Weak transcription	HMEC	breast
38	chr17:19705600-19720800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr17:19706400-19716800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr17:19706800-19769800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr17:19707200-19714400	Strong transcription	Fetal Muscle Leg	muscle
42	chr17:19707400-19726800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr17:19707600-19715200	Weak transcription	Brain Substantia Nigra	brain
44	chr17:19707600-19722800	Weak transcription	Colon Smooth Muscle	Colon
45	chr17:19708000-19715200	Weak transcription	NHDF-Ad	bronchial
46	chr17:19709200-19726600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr17:19709800-19716000	Strong transcription	Adipose Nuclei	Adipose
48	chr17:19709800-19716800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr17:19710000-19714400	Strong transcription	Fetal Lung	lung
50	chr17:19710000-19715800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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