Variant report

Variant	rs17122904
Chromosome Location	chr1:62472142-62472143
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10493315	1.00[CEU][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10493316	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10493317	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12076492	0.81[CHD][hapmap]
rs12084203	0.83[CHB][hapmap]
rs12084877	0.82[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs12562199	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12563258	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17122889	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17122892	1.00[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17122915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122931	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2183995	0.82[CHB][hapmap]
rs2297495	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3762445	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58529158	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59829581	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67035896	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67417917	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67456403	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67526244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67622686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67719504	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67867258	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67967624	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68081851	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72914078	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7538799	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	esv2753481	chr1:62424207-62478878	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv546416	chr1:62437872-62492215	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv999481	chr1:62439219-62472591	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
2	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
3	chr1:62424200-62494200	Weak transcription	Esophagus	oesophagus
4	chr1:62444200-62479200	Weak transcription	Fetal Intestine Small	intestine
5	chr1:62446600-62487600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:62447400-62481200	Weak transcription	Lung	lung
7	chr1:62456200-62478600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:62457000-62473400	Weak transcription	Primary T cells from cord blood	blood
9	chr1:62458800-62521400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:62459000-62484000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:62459000-62516000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:62459000-62530600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:62459200-62487800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:62459200-62511200	Weak transcription	Gastric	stomach
15	chr1:62459200-62550000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:62459400-62479000	Weak transcription	Left Ventricle	heart
17	chr1:62459400-62484000	Weak transcription	Liver	Liver
18	chr1:62459400-62493800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:62459600-62478600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:62459600-62483600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:62459600-62494200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:62459800-62483600	Weak transcription	NHEK	skin
23	chr1:62460000-62478600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:62460000-62499600	Weak transcription	Fetal Intestine Large	intestine
25	chr1:62460000-62516400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:62460000-62544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:62460200-62487600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:62460200-62516000	Weak transcription	HMEC	breast
29	chr1:62461800-62479000	Weak transcription	Psoas Muscle	Psoas
30	chr1:62463200-62472800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:62466400-62494200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:62466800-62477000	Weak transcription	Fetal Brain Female	brain
33	chr1:62468600-62474000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:62469000-62533600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:62469800-62488000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:62471000-62472400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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