Variant report

Variant	rs7212571
Chromosome Location	chr17:20223152-20223153
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:20223140-20223298	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
CCDC144CP	TF binding region
ENSG00000266839	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10491107	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11204300	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11204423	0.84[EUR][1000 genomes]
rs11653630	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11653869	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11654942	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11657161	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11658116	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11868116	0.80[EUR][1000 genomes]
rs11869258	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12453013	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12603372	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12936443	0.80[EUR][1000 genomes]
rs12938355	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12942568	0.87[EUR][1000 genomes]
rs12942627	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12949481	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12950564	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1373146	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16960697	0.80[EUR][1000 genomes]
rs1859407	0.83[EUR][1000 genomes]
rs1974745	0.80[EUR][1000 genomes]
rs1992561	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2013443	0.80[EUR][1000 genomes]
rs2042046	0.80[EUR][1000 genomes]
rs2107565	0.84[EUR][1000 genomes]
rs2158472	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2189709	0.83[EUR][1000 genomes]
rs2526459	0.82[EUR][1000 genomes]
rs2526463	0.83[EUR][1000 genomes]
rs2526465	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2526466	0.91[EUR][1000 genomes]
rs2526476	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2526477	0.89[EUR][1000 genomes]
rs2526478	0.89[EUR][1000 genomes]
rs2526481	0.88[EUR][1000 genomes]
rs2526482	0.87[EUR][1000 genomes]
rs2526486	0.84[EUR][1000 genomes]
rs2703770	0.87[EUR][1000 genomes]
rs2703771	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2703776	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2703777	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2703781	0.89[EUR][1000 genomes]
rs2703786	0.89[EUR][1000 genomes]
rs2703788	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2703795	0.82[EUR][1000 genomes]
rs2703800	0.84[EUR][1000 genomes]
rs2703803	0.85[EUR][1000 genomes]
rs2703805	0.86[EUR][1000 genomes]
rs2703807	0.86[EUR][1000 genomes]
rs2703812	0.86[EUR][1000 genomes]
rs2703814	0.87[EUR][1000 genomes]
rs2703819	0.88[EUR][1000 genomes]
rs28696294	0.83[AFR][1000 genomes]
rs3850779	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3850780	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4925086	0.80[EUR][1000 genomes]
rs4925087	0.80[EUR][1000 genomes]
rs4925090	0.82[EUR][1000 genomes]
rs4925091	0.82[EUR][1000 genomes]
rs55705283	0.80[EUR][1000 genomes]
rs57837691	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62066870	0.82[EUR][1000 genomes]
rs6587219	0.80[EUR][1000 genomes]
rs67217337	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71372302	0.83[AMR][1000 genomes]
rs7211343	0.82[AMR][1000 genomes]
rs7219615	0.88[EUR][1000 genomes]
rs7222987	0.80[EUR][1000 genomes]
rs7223476	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73309111	0.84[ASN][1000 genomes]
rs733794	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs757494	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs757495	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs8071274	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8080649	0.82[EUR][1000 genomes]
rs9898080	0.80[EUR][1000 genomes]
rs9901336	0.82[EUR][1000 genomes]
rs9901796	0.81[EUR][1000 genomes]
rs9907516	0.80[EUR][1000 genomes]
rs9912844	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv520772	chr17:20184501-20522444	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
13	nsv521025	chr17:20198024-20514921	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
14	esv32786	chr17:20219434-20294008	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv471495	chr17:20221409-20464225	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
16	nsv1059504	chr17:20222112-20581021	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7212571	KRT16P3	cis	Esophagus Mucosa	GTEx
rs7212571	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20187800-20223800	Weak transcription	Pancreas	Pancrea
2	chr17:20210800-20223800	Weak transcription	Colonic Mucosa	Colon
3	chr17:20210800-20223800	Weak transcription	Esophagus	oesophagus
4	chr17:20211000-20223800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr17:20211000-20223800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:20211000-20224000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr17:20211000-20224000	Weak transcription	HMEC	breast
8	chr17:20211200-20223800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr17:20211200-20224000	Weak transcription	Fetal Intestine Large	intestine
10	chr17:20211400-20224000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr17:20211600-20224000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr17:20213000-20223800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr17:20213000-20223800	Weak transcription	Adipose Nuclei	Adipose
14	chr17:20213000-20226600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr17:20213200-20223800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr17:20214400-20223400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr17:20217200-20224000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr17:20218400-20223800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr17:20218600-20223800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr17:20218600-20223800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr17:20218600-20223800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr17:20218600-20224000	Weak transcription	A549	lung
23	chr17:20218800-20223800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr17:20218800-20224000	Weak transcription	NHEK	skin
25	chr17:20218800-20224400	Weak transcription	Gastric	stomach
26	chr17:20219000-20223600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr17:20219000-20223800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr17:20219000-20224000	Weak transcription	Brain Germinal Matrix	brain
29	chr17:20219000-20224000	Weak transcription	Spleen	Spleen
30	chr17:20219200-20223600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr17:20219200-20223800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr17:20219200-20223800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr17:20219200-20223800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:20219200-20223800	Weak transcription	Ovary	ovary
35	chr17:20219200-20224000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr17:20219200-20224600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:20219400-20223200	Weak transcription	Hela-S3	cervix
38	chr17:20219400-20223800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr17:20219400-20223800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr17:20219400-20223800	Weak transcription	Aorta	Aorta
41	chr17:20219400-20223800	Weak transcription	Brain Angular Gyrus	brain
42	chr17:20219400-20223800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr17:20219400-20223800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr17:20219400-20223800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr17:20219400-20224000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr17:20219400-20224000	Weak transcription	Fetal Intestine Small	intestine
47	chr17:20219400-20229200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr17:20219600-20223800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr17:20219600-20223800	Weak transcription	Brain Hippocampus Middle	brain
50	chr17:20219600-20223800	Weak transcription	Osteobl	bone

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