Variant report

Variant	rs2231568
Chromosome Location	chr19:36605794-36605795
allele	C/T
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	USF1	chr19:36605551-36606167	A549	lung:	n/a	n/a
2	TAF1	chr19:36605705-36605901	K562	blood:	n/a	n/a
3	HEY1	chr19:36605473-36606959	HepG2	liver:	n/a	chr19:36605499-36605514
4	ELF1	chr19:36605016-36606976	A549	lung:	n/a	chr19:36605886-36605898
5	POLR2A	chr19:36605198-36607300	GM12878	blood:	n/a	n/a
6	ATF2	chr19:36605758-36606171	GM12878	blood:	n/a	n/a
7	MTA3	chr19:36604849-36606294	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:36605518-36606915	GM19099	blood:	n/a	n/a
9	MYC	chr19:36605597-36606582	MCF-7	breast:	n/a	chr19:36605885-36605895 chr19:36605681-36605691 chr19:36605869-36605879
10	POLR2A	chr19:36605269-36606949	GM18505	blood:	n/a	n/a
11	CREB1	chr19:36605618-36605987	A549	lung:	n/a	n/a
12	MAZ	chr19:36605642-36606818	HepG2	liver:	n/a	chr19:36606791-36606801 chr19:36605885-36605895 chr19:36605681-36605691 chr19:36605869-36605879
13	ELF1	chr19:36605531-36607059	MCF-7	breast:	n/a	chr19:36605886-36605898
14	CTCF	chr19:36605740-36605890	HEK293	kidney:	n/a	chr19:36605847-36605863 chr19:36605846-36605864 chr19:36605848-36605869
15	MAX	chr19:36605251-36606591	Hela-S3	cervix:	n/a	chr19:36605493-36605503 chr19:36605885-36605895 chr19:36605681-36605691 chr19:36605869-36605879
16	TCF12	chr19:36605547-36606758	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr19:36605565-36606610	K562	blood:	n/a	n/a
18	HEY1	chr19:36605620-36606211	HepG2	liver:	n/a	n/a
19	GABPA	chr19:36605505-36606777	MCF-7	breast:	n/a	chr19:36606587-36606596 chr19:36606107-36606118 chr19:36606107-36606116 chr19:36606107-36606121 chr19:36606104-36606118 chr19:36606109-36606118
20	BHLHE40	chr19:36605272-36607179	GM12878	blood:	n/a	n/a
21	ELF1	chr19:36605700-36605979	HepG2	liver:	n/a	chr19:36605886-36605898
22	E2F6	chr19:36604839-36606607	K562	blood:	n/a	chr19:36606020-36606034 chr19:36606361-36606370 chr19:36604856-36604865 chr19:36605210-36605219 chr19:36605884-36605893 chr19:36606587-36606596 chr19:36606108-36606117
23	MYC	chr19:36605620-36606458	K562	blood:	n/a	chr19:36605885-36605895 chr19:36605681-36605691 chr19:36605869-36605879
24	MYC	chr19:36605667-36606132	MCF-7	breast:	n/a	chr19:36605885-36605895 chr19:36605681-36605691 chr19:36605869-36605879
25	POLR2A	chr19:36605010-36607073	PANC-1	pancreas:	n/a	n/a
26	SIX5	chr19:36605235-36606624	A549	lung:	n/a	n/a
27	STAT1	chr19:36605541-36606854	GM12878	blood:	n/a	chr19:36606622-36606642 chr19:36606628-36606636 chr19:36606622-36606642 chr19:36606628-36606637 chr19:36606652-36606664 chr19:36606627-36606636 chr19:36606637-36606649
28	E2F6	chr19:36604990-36607379	A549	lung:	n/a	chr19:36606020-36606034 chr19:36606361-36606370 chr19:36605210-36605219 chr19:36605884-36605893 chr19:36606587-36606596 chr19:36606108-36606117
29	ATF3	chr19:36605049-36606612	A549	lung:	n/a	chr19:36605210-36605219 chr19:36606587-36606596
30	POLR2A	chr19:36604904-36606845	PFSK-1	brain:	n/a	n/a
31	MAX	chr19:36605424-36606750	K562	blood:	n/a	chr19:36605493-36605503 chr19:36605885-36605895 chr19:36605681-36605691 chr19:36605869-36605879
32	MAZ	chr19:36604752-36607281	IMR90	lung:	n/a	chr19:36606791-36606801 chr19:36605493-36605503 chr19:36605885-36605895 chr19:36605681-36605691 chr19:36605869-36605879
33	REST	chr19:36605604-36606033	HepG2	liver:	n/a	chr19:36605622-36605635
34	USF2	chr19:36605640-36606128	H1-hESC	embryonic stem cell:	n/a	n/a
35	CEBPB	chr19:36605676-36606243	Hela-S3	cervix:	n/a	n/a
36	ATF3	chr19:36605333-36606658	A549	lung:	n/a	chr19:36606587-36606596
37	POLR2A	chr19:36605336-36606246	H1-hESC	embryonic stem cell:	n/a	n/a
38	REST	chr19:36605771-36605866	PANC-1	pancreas:	n/a	n/a
39	E2F6	chr19:36604762-36606635	H1-hESC	embryonic stem cell:	n/a	chr19:36606020-36606034 chr19:36606361-36606370 chr19:36604856-36604865 chr19:36605210-36605219 chr19:36605884-36605893 chr19:36606587-36606596 chr19:36606108-36606117
40	TAF1	chr19:36605351-36607052	HepG2	liver:	n/a	n/a
41	TCF12	chr19:36605670-36605965	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr19:36604905-36607077	MCF-7	breast:	n/a	n/a
43	ZBTB33	chr19:36605164-36606642	A549	lung:	n/a	n/a
44	POLR2A	chr19:36605255-36606778	MCF-7	breast:	n/a	n/a
45	EP300	chr19:36605776-36606460	HepG2	liver:	n/a	chr19:36605865-36605881
46	MAX	chr19:36604753-36607476	A549	lung:	n/a	chr19:36606791-36606801 chr19:36605493-36605503 chr19:36605885-36605895 chr19:36605681-36605691 chr19:36605869-36605879
47	POLR2A	chr19:36605544-36606210	HepG2	liver:	n/a	n/a
48	RELA	chr19:36605569-36606885	GM12892	blood:	n/a	n/a
49	TAF1	chr19:36605484-36606616	H1-hESC	embryonic stem cell:	n/a	n/a
50	CBX3	chr19:36605656-36606313	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36603757..36607457-chr19:36664359..36667558,3	MCF-7	breast:
2	chr19:36605358..36605965-chr21:37802132..37802835,2	Hela-S3	cervix:
3	chr19:36604314..36608037-chr19:36629557..36633745,12	MCF-7	breast:
4	chr1:94146477..94147235-chr19:36605467..36606382,2	Hela-S3	cervix:
5	chr13:111365280..111366051-chr19:36605506..36606391,2	Hela-S3	cervix:
6	chr19:36604785..36608680-chr19:36610341..36613498,5	K562	blood:
7	chr16:85784651..85786943-chr19:36604623..36606836,2	MCF-7	breast:
8	chr19:36543835..36550918-chr19:36603651..36608049,11	MCF-7	breast:
9	chr19:36604617..36608522-chr19:36628102..36632329,9	MCF-7	breast:
10	chr19:36604026..36607708-chr19:36630473..36633466,10	K562	blood:
11	chr19:36605206..36606094-chr6:26056170..26056718,2	Hela-S3	cervix:
12	chr19:36605408..36606315-chr2:9983471..9984383,2	Hela-S3	cervix:
13	chr19:36544216..36546740-chr19:36604520..36606743,4	K562	blood:
14	chr19:36604594..36608993-chr19:36628830..36633466,13	K562	blood:
15	chr19:36545240..36547330-chr19:36604696..36606743,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBCB-1	chr19:36605264-36606048	NONHSAT065958

Variant related genes	Relation type
POLR2I	TF binding region
TBCB	TF binding region
ENSG00000134905	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000267005	Chromatin interaction
ENSG00000075702	Chromatin interaction
ENSG00000105254	Chromatin interaction
ENSG00000115750	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000154102	Chromatin interaction
ENSG00000230479	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000161277	Chromatin interaction
ENSG00000153487	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1009381	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10406862	0.92[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap]
rs10418079	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10419924	0.86[ASN][1000 genomes]
rs10420345	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10421377	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10422055	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10425700	0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs10853945	0.83[EUR][1000 genomes]
rs11666192	0.84[ASN][1000 genomes]
rs11669890	0.82[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs11879369	0.86[EUR][1000 genomes]
rs12462159	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs12608517	0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs12971639	0.89[EUR][1000 genomes]
rs12971936	0.91[EUR][1000 genomes]
rs12972828	0.89[EUR][1000 genomes]
rs12981698	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12982375	0.83[EUR][1000 genomes]
rs1548506	0.83[EUR][1000 genomes]
rs2023866	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2051800	0.81[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs2074435	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2075472	0.84[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2141959	0.82[ASN][1000 genomes]
rs2227260	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301734	0.92[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2301737	0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2871649	0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs3810447	0.90[EUR][1000 genomes]
rs4555271	0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs4806249	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs4806254	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs4806262	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4806269	0.81[EUR][1000 genomes]
rs4806273	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4806276	0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs7250364	0.84[ASN][1000 genomes]
rs7251912	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs7257026	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7258807	0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs73036134	0.83[ASN][1000 genomes]
rs757223	0.81[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs8104047	0.92[EUR][1000 genomes]
rs8104053	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2231568	POLR2I///RPSA	Cis_1M	lymphoblastoid	RTeQTL
rs2231568	PHLDB3	cis	cerebellum	SCAN
rs2231568	PHLDB3	cis	parietal	SCAN
rs2231568	LOC390940	cis	parietal	SCAN
rs2231568	CYP2A7	cis	parietal	SCAN
rs2231568	CYP2A7	cis	cerebellum	SCAN
rs2231568	PSG9	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36604000-36608000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:36604400-36605800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr19:36604400-36607000	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr19:36604400-36607200	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:36604400-36607200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr19:36604400-36607400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr19:36604400-36607400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr19:36604600-36606000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr19:36604600-36606000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:36604600-36606200	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr19:36604600-36606200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:36604600-36606200	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr19:36604600-36606200	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr19:36604600-36607000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:36604600-36607000	Active TSS	Fetal Intestine Small	intestine
16	chr19:36604600-36607000	Active TSS	HSMMtube	muscle
17	chr19:36604600-36607200	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr19:36604600-36607200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:36604600-36607200	Active TSS	Fetal Kidney	kidney
20	chr19:36604800-36605800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr19:36604800-36605800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:36604800-36605800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:36604800-36605800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr19:36604800-36605800	Flanking Active TSS	HSMM	muscle
25	chr19:36604800-36606000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr19:36604800-36606000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr19:36604800-36606200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr19:36604800-36606200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr19:36604800-36606200	Flanking Active TSS	Fetal Thymus	thymus
30	chr19:36604800-36606200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr19:36604800-36607000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:36604800-36607000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:36604800-36607000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:36604800-36607000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:36604800-36607000	Active TSS	Ovary	ovary
36	chr19:36604800-36607000	Active TSS	A549	lung
37	chr19:36604800-36607000	Active TSS	GM12878-XiMat	blood
38	chr19:36604800-36607200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr19:36604800-36607200	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr19:36604800-36607200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr19:36604800-36607200	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr19:36604800-36607200	Active TSS	NHDF-Ad	bronchial
43	chr19:36604800-36607600	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr19:36605000-36606200	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr19:36605000-36606200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr19:36605000-36606800	Active TSS	Fetal Intestine Large	intestine
47	chr19:36605000-36606800	Active TSS	NHEK	skin
48	chr19:36605000-36607000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:36605000-36607000	Active TSS	Colon Smooth Muscle	Colon
50	chr19:36605000-36607000	Active TSS	Stomach Mucosa	stomach

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