Variant report

Variant	rs34896171
Chromosome Location	chr1:62428732-62428733
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10889273	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585194	0.90[ASN][1000 genomes]
rs11801995	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11804927	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11810455	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059237	0.82[AMR][1000 genomes]
rs12059478	0.82[AMR][1000 genomes]
rs12090332	0.82[AMR][1000 genomes]
rs12724144	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12725114	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12725290	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12731388	0.85[AMR][1000 genomes]
rs12731725	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12735117	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12738266	0.82[AMR][1000 genomes]
rs12740631	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12748525	0.90[ASN][1000 genomes]
rs12749323	0.85[AMR][1000 genomes]
rs12749575	0.85[AMR][1000 genomes]
rs12749947	0.85[AMR][1000 genomes]
rs12753261	0.83[AMR][1000 genomes]
rs12753435	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12756068	0.85[AMR][1000 genomes]
rs1556482	0.85[AMR][1000 genomes]
rs1556483	0.85[AMR][1000 genomes]
rs1556484	0.85[AMR][1000 genomes]
rs1556485	0.85[AMR][1000 genomes]
rs17122871	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122873	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17313118	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17378746	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17382499	0.82[AMR][1000 genomes]
rs17386553	0.85[AMR][1000 genomes]
rs2365734	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2482893	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2482894	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2498973	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2498975	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886446	0.89[EUR][1000 genomes]
rs2990508	0.90[ASN][1000 genomes]
rs34115734	0.85[AMR][1000 genomes]
rs34158435	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34189113	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34843158	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34935930	0.85[AMR][1000 genomes]
rs34986631	0.82[AMR][1000 genomes]
rs35523060	0.82[AMR][1000 genomes]
rs35663562	0.85[AMR][1000 genomes]
rs35702885	0.85[AMR][1000 genomes]
rs35814605	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35899620	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36125117	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3762447	0.85[AMR][1000 genomes]
rs56033850	0.85[AMR][1000 genomes]
rs66472440	0.82[AMR][1000 genomes]
rs66606678	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6667051	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6678412	0.82[AMR][1000 genomes]
rs6685239	0.82[AMR][1000 genomes]
rs67187546	0.83[AMR][1000 genomes]
rs67395722	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67412592	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67439419	0.85[AMR][1000 genomes]
rs67695689	0.85[AMR][1000 genomes]
rs67786436	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72677923	0.85[AMR][1000 genomes]
rs72677926	0.82[AMR][1000 genomes]
rs7514549	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7517453	0.85[AMR][1000 genomes]
rs7520931	0.90[ASN][1000 genomes]
rs7526627	0.85[AMR][1000 genomes]
rs7529379	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543658	0.83[AMR][1000 genomes]
rs7543741	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1110	chr1:62395723-62454435	Enhancers Weak transcription 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
7	nsv546415	chr1:62405873-62437872	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	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
9	nsv437210	chr1:62419727-62448245	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	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
11	nsv1010655	chr1:62427826-62447302	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
2	chr1:62406600-62430200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:62409000-62436800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:62409200-62456000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:62409200-62456800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:62409200-62457000	Weak transcription	Fetal Intestine Large	intestine
7	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
8	chr1:62409400-62429600	Weak transcription	Gastric	stomach
9	chr1:62409400-62458400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:62417800-62431600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:62418000-62428800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:62418200-62446400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:62418400-62441400	Weak transcription	Fetal Kidney	kidney
14	chr1:62418600-62432400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:62418600-62432400	Weak transcription	NHEK	skin
16	chr1:62418800-62432800	Weak transcription	HMEC	breast
17	chr1:62419600-62445800	Weak transcription	Left Ventricle	heart
18	chr1:62420800-62429800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:62422800-62432600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:62423400-62431200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:62423400-62433600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:62423600-62433800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:62423800-62432800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:62424000-62432000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:62424200-62436600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:62424200-62494200	Weak transcription	Esophagus	oesophagus
27	chr1:62424800-62438200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:62425000-62441400	Weak transcription	Stomach Mucosa	stomach
29	chr1:62427200-62432800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:62428400-62430600	Strong transcription	Fetal Intestine Small	intestine

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