Variant report

Variant	rs73044947
Chromosome Location	chr19:38893289-38893290
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	YY1	chr19:38893117-38894435	K562	blood:	n/a	chr19:38893702-38893716 chr19:38893945-38893954
2	CTCF	chr19:38893103-38894443	SK-N-SH	brain:	n/a	chr19:38893765-38893775 chr19:38893763-38893772 chr19:38893763-38893776 chr19:38893947-38893960 chr19:38893763-38893776 chr19:38893760-38893778 chr19:38893904-38893917 chr19:38893761-38893777 chr19:38893569-38893579
3	CREB1	chr19:38893223-38894059	H1-hESC	embryonic stem cell:	n/a	n/a
4	ATF3	chr19:38893164-38893988	A549	lung:	n/a	chr19:38893945-38893954
5	RAD21	chr19:38893234-38894074	A549	lung:	n/a	chr19:38893904-38893914 chr19:38893766-38893776 chr19:38893902-38893914 chr19:38893761-38893780
6	REST	chr19:38893208-38894484	A549	lung:	n/a	chr19:38893565-38893575 chr19:38893873-38893886 chr19:38893889-38893902
7	YY1	chr19:38893284-38893942	H1-hESC	embryonic stem cell:	n/a	chr19:38893702-38893716
8	TCF7L2	chr19:38893254-38894172	HCT-116	colon:	n/a	n/a
9	SIN3AK20	chr19:38893191-38894231	A549	lung:	n/a	n/a
10	TCF12	chr19:38893028-38894554	A549	lung:	n/a	n/a
11	YY1	chr19:38893263-38893613	GM12892	blood:	n/a	n/a
12	RCOR1	chr19:38893227-38894434	K562	blood:	n/a	n/a
13	BCLAF1	chr19:38893178-38893599	GM12878	blood:	n/a	n/a
14	CREB1	chr19:38893243-38894020	K562	blood:	n/a	n/a
15	SP1	chr19:38893266-38894016	H1-hESC	embryonic stem cell:	n/a	chr19:38893943-38893955 chr19:38893945-38893954 chr19:38893944-38893953 chr19:38893944-38893958 chr19:38893605-38893616 chr19:38893944-38893953 chr19:38893943-38893955 chr19:38893743-38893752
16	HEY1	chr19:38893284-38894021	HepG2	liver:	n/a	n/a
17	CREB1	chr19:38893286-38894181	GM12878	blood:	n/a	n/a
18	ZC3H11A	chr19:38893247-38893865	K562	blood:	n/a	n/a
19	NFYB	chr19:38893220-38894186	K562	blood:	n/a	chr19:38893648-38893663 chr19:38893686-38893701 chr19:38893687-38893701 chr19:38893690-38893702 chr19:38893686-38893701 chr19:38893688-38893703 chr19:38893689-38893699 chr19:38893648-38893663
20	CTCF	chr19:38893240-38893390	HPF	lung:	n/a	n/a
21	ELF1	chr19:38893282-38894055	K562	blood:	n/a	n/a
22	POLR2A	chr19:38893169-38894164	PFSK-1	brain:	n/a	n/a
23	CTCF	chr19:38891235-38894621	A549	lung:	n/a	chr19:38893765-38893775 chr19:38893763-38893772 chr19:38893763-38893776 chr19:38893947-38893960 chr19:38893763-38893776 chr19:38893760-38893778 chr19:38893904-38893917 chr19:38893761-38893777 chr19:38893569-38893579
24	MAX	chr19:38893216-38894520	MCF-7	breast:	n/a	chr19:38894146-38894156 chr19:38893956-38893966 chr19:38893946-38893956 chr19:38894160-38894169
25	YY1	chr19:38893162-38894486	HepG2	liver:	n/a	chr19:38893702-38893716 chr19:38893945-38893954
26	RCOR1	chr19:38893279-38893985	GM12878	blood:	n/a	n/a
27	E2F6	chr19:38893242-38894405	K562	blood:	n/a	chr19:38893769-38893778 chr19:38893945-38893954 chr19:38893675-38893686
28	ELF1	chr19:38893276-38894094	A549	lung:	n/a	n/a
29	USF1	chr19:38893280-38894016	A549	lung:	n/a	n/a
30	NR2F2	chr19:38893084-38893684	K562	blood:	n/a	n/a
31	POLR2A	chr19:38893205-38894460	H1-neurons	neurons:	n/a	n/a
32	MYC	chr19:38893265-38894446	K562	blood:	n/a	chr19:38894146-38894156 chr19:38893956-38893966 chr19:38893946-38893956 chr19:38894160-38894169
33	POLR2A	chr19:38893278-38894427	K562	blood:	n/a	n/a
34	FOSL2	chr19:38893152-38894206	A549	lung:	n/a	chr19:38894152-38894161 chr19:38893652-38893661
35	POLR2A	chr19:38893243-38893972	HUVEC	blood vessel:	n/a	n/a
36	MTA3	chr19:38893216-38893550	GM12878	blood:	n/a	n/a
37	RAD21	chr19:38893286-38894045	H1-hESC	embryonic stem cell:	n/a	chr19:38893904-38893914 chr19:38893766-38893776 chr19:38893902-38893914 chr19:38893761-38893780
38	REST	chr19:38893042-38894554	H1-neurons	neurons:	n/a	chr19:38893565-38893575 chr19:38893873-38893886 chr19:38893889-38893902
39	SIN3AK20	chr19:38893137-38894342	MCF-7	breast:	n/a	n/a
40	POLR2A	chr19:38887005-38894478	MCF10A-Er-Src	breast:	n/a	n/a
41	YY1	chr19:38893191-38894179	GM12891	blood:	n/a	chr19:38893702-38893716 chr19:38893945-38893954
42	POLR2A	chr19:38893285-38893385	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAX	chr19:38893065-38894637	A549	lung:	n/a	chr19:38894146-38894156 chr19:38893956-38893966 chr19:38893946-38893956 chr19:38894160-38894169
44	RAD21	chr19:38893279-38894093	MCF-7	breast:	n/a	chr19:38893904-38893914 chr19:38893766-38893776 chr19:38893902-38893914 chr19:38893761-38893780
45	POLR2A	chr19:38893168-38894518	K562	blood:	n/a	n/a
46	POLR2A	chr19:38893191-38894107	U87	brain:	n/a	n/a
47	POLR2A	chr19:38893282-38894169	HCT-116	colon:	n/a	n/a
48	GATA3	chr19:38893165-38894540	A549	lung:	n/a	n/a
49	SIX5	chr19:38893048-38894250	A549	lung:	n/a	n/a
50	ZNF263	chr19:38893181-38894458	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38890926..38893595-chr19:38978170..38979921,2	K562	blood:
2	chr19:38892832..38895683-chr19:38905614..38908476,2	K562	blood:
3	chr19:38892751..38895518-chr19:38905731..38908056,2	MCF-7	breast:
4	chr19:38864731..38867116-chr19:38892888..38894994,2	MCF-7	breast:
5	chr19:38864536..38866994-chr19:38891927..38895682,4	MCF-7	breast:
6	chr19:38825542..38827860-chr19:38892803..38895034,2	K562	blood:
7	chr19:38886501..38890187-chr19:38891290..38894154,6	MCF-7	breast:
8	chr19:38724234..38725570-chr19:38893025..38893769,4	K562	blood:
9	chr19:38893264..38895978-chr19:39340017..39342861,2	MCF-7	breast:
10	chr19:38873942..38878444-chr19:38892255..38895006,5	K562	blood:
11	chr19:38891109..38897587-chr19:38900077..38906045,7	MCF-7	breast:
12	chr19:38892840..38895111-chr19:38906916..38908853,2	MCF-7	breast:
13	chr19:38810024..38812525-chr19:38892478..38895075,3	MCF-7	breast:
14	chr19:38891977..38893968-chr19:38915428..38917384,2	K562	blood:
15	chr19:38878160..38880019-chr19:38892423..38895031,2	MCF-7	breast:

Variant related genes	Relation type
FAM98C	TF binding region
ENSG00000171777	Chromatin interaction
ENSG00000267090	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000099337	Chromatin interaction
ENSG00000267473	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11083454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11538289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2302228	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28384479	0.85[ASN][1000 genomes]
rs3745955	0.80[EUR][1000 genomes]
rs3745963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760884	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57753437	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59491640	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60780508	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508791	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6508792	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6508793	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246191	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246213	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248540	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248780	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7257976	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043029	0.81[EUR][1000 genomes]
rs73043030	0.93[EUR][1000 genomes]
rs73043033	0.93[EUR][1000 genomes]
rs73043098	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73044905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044908	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044911	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044915	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044917	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044919	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044923	0.80[EUR][1000 genomes]
rs73044926	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044930	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73044948	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8108440	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8109713	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8112499	1.00[AMR][1000 genomes];1.00[EUR][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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv911661	chr19:38872335-38894829	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv911662	chr19:38872634-38895809	Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1803709	chr19:38874828-38900078	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38883600-38893400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:38891200-38893400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:38891600-38893400	Enhancers	Stomach Mucosa	stomach
4	chr19:38892600-38893800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:38893000-38894400	Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr19:38893200-38893400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
7	chr19:38893200-38893400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr19:38893200-38893400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:38893200-38893400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:38893200-38893400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr19:38893200-38893400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr19:38893200-38893400	Flanking Active TSS	Primary B cells from peripheral blood	blood
13	chr19:38893200-38893400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr19:38893200-38893400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr19:38893200-38893400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr19:38893200-38893400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:38893200-38893400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr19:38893200-38893400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr19:38893200-38893400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr19:38893200-38893400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:38893200-38893400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:38893200-38893400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:38893200-38893400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:38893200-38893400	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr19:38893200-38893400	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr19:38893200-38893400	Flanking Active TSS	Brain Germinal Matrix	brain
27	chr19:38893200-38893400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
28	chr19:38893200-38893400	Flanking Active TSS	Colonic Mucosa	Colon
29	chr19:38893200-38893400	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr19:38893200-38893400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr19:38893200-38893400	Flanking Active TSS	Fetal Brain Female	brain
32	chr19:38893200-38893400	Flanking Active TSS	Fetal Heart	heart
33	chr19:38893200-38893400	Flanking Active TSS	Fetal Intestine Large	intestine
34	chr19:38893200-38893400	Flanking Active TSS	Fetal Intestine Small	intestine
35	chr19:38893200-38893400	Flanking Active TSS	Fetal Stomach	stomach
36	chr19:38893200-38893400	Flanking Active TSS	Fetal Thymus	thymus
37	chr19:38893200-38893400	Flanking Active TSS	Pancreas	Pancrea
38	chr19:38893200-38893400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
39	chr19:38893200-38893400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr19:38893200-38893400	Flanking Active TSS	Thymus	Thymus
41	chr19:38893200-38893400	Flanking Active TSS	A549	lung
42	chr19:38893200-38893400	Flanking Active TSS	HepG2	liver
43	chr19:38893200-38893400	Flanking Active TSS	K562	blood
44	chr19:38893200-38893400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr19:38893200-38893400	Flanking Active TSS	NHEK	skin
46	chr19:38893200-38893400	Flanking Active TSS	Osteobl	bone
47	chr19:38893200-38893600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:38893200-38893600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr19:38893200-38893600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr19:38893200-38893600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links