Variant report

Variant	rs11657161
Chromosome Location	chr17:20180715-20180716
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10491107	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204300	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204423	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11653630	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11653869	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11654942	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11658116	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11868116	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11869258	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12453013	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12603372	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936443	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12938355	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12942568	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12942627	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12949481	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12950564	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1373146	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16960697	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1859407	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1974745	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1992561	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2013443	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2042046	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2107565	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2158472	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2189709	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2526459	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2526463	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2526465	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2526466	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2526476	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2526477	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2526478	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2526481	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2526482	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2526486	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703770	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2703771	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2703776	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2703777	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2703781	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2703786	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2703788	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2703795	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703800	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703803	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2703805	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2703807	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2703812	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2703814	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2703819	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3850779	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3850780	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925086	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4925087	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4925090	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4925091	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55705283	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57837691	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066865	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62066870	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6587060	0.84[ASN][1000 genomes]
rs6587219	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67217337	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7212500	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7212571	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7216599	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7216794	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7219615	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7219908	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7222984	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7222987	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7223476	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73309111	0.89[ASN][1000 genomes]
rs733794	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs757494	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs757495	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8066143	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8071274	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8078716	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8080649	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9893832	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9898080	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9901336	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9901796	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9902032	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9907516	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9912844	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv428669	chr17:20071969-20245033	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1064854	chr17:20086562-20225751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv2761953	chr17:20086562-20225763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1063833	chr17:20088333-20206601	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv574581	chr17:20088492-20699545	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
12	nsv1062124	chr17:20139384-20206601	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv543261	chr17:20139384-20206601	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv1065758	chr17:20141912-20464366	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
15	nsv543262	chr17:20141912-20464366	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
16	nsv1057389	chr17:20158343-20256498	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv427993	chr17:20171398-20482061	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
18	nsv916440	chr17:20171468-20839266	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11657161	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs11657161	KRT16P3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20136400-20209800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:20151600-20190000	Weak transcription	Colonic Mucosa	Colon
3	chr17:20162000-20187600	Weak transcription	Pancreas	Pancrea
4	chr17:20164000-20200200	Weak transcription	Fetal Intestine Large	intestine
5	chr17:20164000-20205600	Weak transcription	Esophagus	oesophagus
6	chr17:20164200-20200200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr17:20164400-20202200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr17:20164600-20203800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr17:20164600-20204000	Weak transcription	Gastric	stomach
10	chr17:20165000-20182000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr17:20166000-20185000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr17:20166600-20187400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr17:20167200-20183200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr17:20167400-20187600	Weak transcription	A549	lung
15	chr17:20167400-20200200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr17:20168200-20182000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr17:20168200-20182400	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr17:20170000-20182000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr17:20170400-20209600	Weak transcription	HMEC	breast
20	chr17:20171200-20200200	Weak transcription	Lung	lung
21	chr17:20171400-20187400	Weak transcription	HSMM	muscle
22	chr17:20171400-20187800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr17:20171600-20181600	Weak transcription	HSMMtube	muscle
24	chr17:20171600-20183800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr17:20173400-20187600	Weak transcription	Aorta	Aorta
26	chr17:20173400-20197600	Weak transcription	Brain Germinal Matrix	brain
27	chr17:20174400-20200200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr17:20174800-20188400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr17:20175000-20181600	Weak transcription	Osteobl	bone
30	chr17:20175000-20187800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr17:20175000-20200200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr17:20176400-20183000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr17:20176400-20183000	Weak transcription	Fetal Intestine Small	intestine
34	chr17:20176600-20182800	Weak transcription	Fetal Brain Female	brain
35	chr17:20176800-20184400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr17:20177000-20184400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr17:20177000-20184400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr17:20177000-20184400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr17:20177400-20181400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr17:20177400-20181600	Weak transcription	NH-A	brain
41	chr17:20177400-20182200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr17:20177600-20181600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr17:20177600-20182400	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr17:20177800-20183200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr17:20178600-20185200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr17:20179000-20180800	Enhancers	Fetal Thymus	thymus
47	chr17:20179000-20181000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr17:20179000-20181200	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr17:20179000-20181400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr17:20179000-20182400	Enhancers	Primary T cells fromperipheralblood	blood

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