Variant report

Variant	rs17318596
Chromosome Location	chr19:41937095-41937096
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41936747-41937220	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr19:41936242-41939720	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:41937050-41937103	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr19:41936665-41938558	A549	lung:	n/a	n/a
5	POLR2A	chr19:41936847-41938776	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr19:41936833-41937144	A549	lung:	n/a	n/a
7	POLR2A	chr19:41936873-41937132	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:41936733-41937183	GM12892	blood:	n/a	n/a
9	POLR2A	chr19:41936748-41937226	K562	blood:	n/a	n/a
10	POLR2A	chr19:41936823-41937169	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:41936609-41937211	GM12892	blood:	n/a	n/a
12	POLR2A	chr19:41936921-41937109	A549	lung:	n/a	n/a
13	POLR2A	chr19:41936589-41937558	K562	blood:	n/a	n/a
14	POLR2A	chr19:41936772-41939698	K562	blood:	n/a	n/a
15	POLR2A	chr19:41936609-41939024	K562	blood:	n/a	n/a
16	POLR2A	chr19:41936804-41937251	HL-60	blood:	n/a	n/a
17	POLR2A	chr19:41936662-41937156	GM12892	blood:	n/a	n/a
18	POLR2A	chr19:41936816-41937125	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr19:41937013-41937176	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr19:41936850-41937146	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41936622..41939586-chr19:41947612..41949294,2	K562	blood:
2	chr19:41903978..41906376-chr19:41936347..41938650,2	K562	blood:
3	chr19:41936691..41939385-chr19:41940971..41942681,2	K562	blood:
4	chr19:41932170..41934404-chr19:41937034..41938933,2	MCF-7	breast:
5	chr19:41858044..41860036-chr19:41936343..41938976,2	MCF-7	breast:
6	chr19:41932975..41939032-chr19:41942824..41947362,11	K562	blood:
7	chr19:41869689..41871301-chr19:41934522..41938582,3	MCF-7	breast:
8	chr19:41854997..41857882-chr19:41936473..41939434,2	K562	blood:
9	chr19:41935462..41938566-chr19:41944097..41946991,4	MCF-7	breast:
10	chr19:41927679..41929725-chr19:41935505..41937205,2	MCF-7	breast:

No data

Variant related genes	Relation type
B3GNT8	TF binding region
ENSG00000142046	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000105341	Chromatin interaction
ENSG00000123810	Chromatin interaction
ENSG00000204978	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000177191	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000268987	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10409485	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10413735	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10416743	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10417311	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10417997	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10420556	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10422783	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10422956	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10432268	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1043413	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1077856	0.84[ASN][1000 genomes]
rs10853751	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11083618	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11083619	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11667848	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11667908	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11668924	0.80[ASN][1000 genomes]
rs11670583	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11670668	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11670757	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11880539	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11883104	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12602	0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12709849	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12980966	0.83[ASN][1000 genomes]
rs13344547	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13344563	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13345590	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13346603	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1473248	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs166925	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16975238	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17318666	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1967333	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1967334	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2231935	0.80[AMR][1000 genomes]
rs2231940	0.89[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241706	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241707	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241708	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241709	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241710	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241711	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288871	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2304242	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304243	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2317131	0.84[ASN][1000 genomes]
rs2569400	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2569754	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs284648	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284649	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284650	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284651	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284652	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284654	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284655	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284656	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284657	0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs284658	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs284660	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284661	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284662	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284663	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3213860	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3213861	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3745290	0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3745292	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3786553	0.88[ASN][1000 genomes]
rs3810174	1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3810175	1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816037	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3826713	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4605279	0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4674	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802116	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802117	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802118	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803461	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803462	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803463	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803465	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4803467	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803468	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803469	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55986560	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58961854	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62117461	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62117462	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6508977	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7247332	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7255918	0.84[ASN][1000 genomes]
rs7258973	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8103531	0.80[EUR][1000 genomes]
rs8105833	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs878082	1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs878083	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs892044	1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs9304593	1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant related diseases (count:1)

Disease	PMID	Source
Height	20881960	GWAS catalog

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs17318596	PSG2	cis	parietal	SCAN
rs17318596	BCKDHA	trans	parietal	SCAN
rs17318596	ZNF233	cis	cerebellum	SCAN
rs17318596	LHB	cis	parietal	SCAN
rs17318596	PHLDB3	cis	parietal	SCAN
rs17318596	ATP5SL	cis	lymphoblastoid	seeQTL
rs17318596	MEGF8	cis	parietal	SCAN
rs17318596	NOSIP	cis	parietal	SCAN
rs17318596	PVR	cis	parietal	SCAN
rs17318596	B3GALT7	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41933200-41938200	Weak transcription	Fetal Kidney	kidney
2	chr19:41933800-41938000	Weak transcription	Psoas Muscle	Psoas
3	chr19:41934000-41944800	Weak transcription	Hela-S3	cervix
4	chr19:41934200-41937200	Weak transcription	HepG2	liver
5	chr19:41934200-41937400	Weak transcription	Ovary	ovary
6	chr19:41934200-41937600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:41934200-41938000	Weak transcription	Osteobl	bone
8	chr19:41934200-41938200	Weak transcription	Brain Angular Gyrus	brain
9	chr19:41934400-41939600	Strong transcription	Brain Germinal Matrix	brain
10	chr19:41934400-41945000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:41934600-41937400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr19:41934600-41937400	Weak transcription	NHLF	lung
13	chr19:41934600-41937600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:41934600-41937600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr19:41934600-41938000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr19:41934600-41938200	Weak transcription	NH-A	brain
17	chr19:41934600-41938200	Weak transcription	NHDF-Ad	bronchial
18	chr19:41934600-41944200	Weak transcription	Fetal Brain Male	brain
19	chr19:41934800-41937200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:41934800-41937200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr19:41934800-41937600	Weak transcription	Fetal Lung	lung
22	chr19:41934800-41937600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr19:41934800-41938200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:41934800-41939600	Strong transcription	Fetal Brain Female	brain
25	chr19:41934800-41945400	Weak transcription	Small Intestine	intestine
26	chr19:41935000-41937200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr19:41935000-41937200	Weak transcription	Brain Hippocampus Middle	brain
28	chr19:41935000-41937600	Weak transcription	HMEC	breast
29	chr19:41935000-41937800	Weak transcription	Aorta	Aorta
30	chr19:41935000-41937800	Weak transcription	Stomach Mucosa	stomach
31	chr19:41935000-41940000	Strong transcription	Fetal Stomach	stomach
32	chr19:41935000-41945000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:41935200-41937200	Weak transcription	Primary B cells from cord blood	blood
34	chr19:41935200-41937200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr19:41935200-41937400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr19:41935200-41937400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr19:41935200-41938000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr19:41935200-41938000	Weak transcription	K562	blood
39	chr19:41935400-41937600	Weak transcription	GM12878-XiMat	blood
40	chr19:41935400-41937800	Weak transcription	Brain Substantia Nigra	brain
41	chr19:41935400-41938200	Weak transcription	HUVEC	blood vessel
42	chr19:41935400-41938400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr19:41935600-41937200	Strong transcription	Fetal Intestine Small	intestine
44	chr19:41935600-41937600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr19:41936000-41937800	Strong transcription	Fetal Intestine Large	intestine
46	chr19:41936000-41938400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:41936200-41940000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:41936400-41939000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:41936400-41939400	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:41936400-41939600	Strong transcription	Dnd41	blood

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