Variant report

Variant	rs1002640
Chromosome Location	chr19:18512575-18512576
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	ELF1	chr19:18512362-18512943	MCF-7	breast:	n/a	chr19:18512837-18512848
2	CTCF	chr19:18512452-18512879	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr19:18512540-18512690	WERI-Rb-1	eye:	n/a	n/a
4	CBX3	chr19:18512348-18512905	K562	blood:	n/a	n/a
5	CTCF	chr19:18512520-18512670	HVMF	connective:	n/a	n/a
6	SPI1	chr19:18512573-18513057	K562	blood:	n/a	chr19:18512837-18512850 chr19:18512839-18512848 chr19:18512836-18512849
7	CTCF	chr19:18512540-18512690	RPTEC	kidney:	n/a	n/a
8	GABPA	chr19:18512357-18512890	MCF-7	breast:	n/a	n/a
9	RAD21	chr19:18512488-18512892	SK-N-SH_RA	brain:	n/a	chr19:18512861-18512875
10	SMC3	chr19:18512515-18512891	Hela-S3	cervix:	n/a	n/a
11	MAZ	chr19:18512549-18512908	K562	blood:	n/a	n/a
12	CTCF	chr19:18512563-18512818	GM12892	blood:	n/a	n/a
13	CTCF	chr19:18512560-18512710	GM12864	blood:	n/a	n/a
14	FOXA1	chr19:18512376-18512791	HepG2	liver:	n/a	n/a
15	GABPA	chr19:18512372-18512890	HL-60	blood:	n/a	n/a
16	SPI1	chr19:18512237-18513276	GM12878	blood:	n/a	chr19:18512837-18512850 chr19:18512839-18512848 chr19:18512836-18512849
17	CTCF	chr19:18512539-18512813	HepG2	liver:	n/a	n/a
18	STAT5A	chr19:18512408-18513063	GM12878	blood:	n/a	n/a
19	KAP1	chr19:18512424-18512713	U2OS	brain:	n/a	n/a
20	RUNX3	chr19:18512347-18512932	GM12878	blood:	n/a	n/a
21	TCF12	chr19:18512253-18512942	A549	lung:	n/a	n/a
22	CTCF	chr19:18512565-18512801	GM19239	blood:	n/a	n/a
23	GABPA	chr19:18512431-18512786	MCF-7	breast:	n/a	n/a
24	GABPA	chr19:18512385-18512814	A549	lung:	n/a	n/a
25	SPI1	chr19:18512483-18512986	K562	blood:	n/a	chr19:18512837-18512850 chr19:18512839-18512848 chr19:18512836-18512849
26	EP300	chr19:18512533-18512887	GM12878	blood:	n/a	chr19:18512822-18512836 chr19:18512823-18512832
27	CTCF	chr19:18512560-18512710	NHEK	skin:	n/a	n/a
28	ARID3A	chr19:18512523-18512763	HepG2	liver:	n/a	n/a
29	CTCF	chr19:18512530-18512798	A549	lung:	n/a	n/a
30	CTCF	chr19:18512560-18512710	WI-38	lung:	n/a	n/a
31	RCOR1	chr19:18512403-18512960	GM12878	blood:	n/a	n/a
32	CTCF	chr19:18512540-18512690	HFF	foreskin:	n/a	n/a
33	ZNF263	chr19:18512461-18512775	HEK293-T-REx	kidney:	n/a	n/a
34	NFIC	chr19:18512395-18512932	GM12878	blood:	n/a	n/a
35	SPI1	chr19:18512356-18513065	HL-60	blood:	n/a	chr19:18512837-18512850 chr19:18512839-18512848 chr19:18512836-18512849
36	CTCF	chr19:18512560-18512710	NHLF	lung:	n/a	n/a
37	ZNF143	chr19:18512522-18512879	GM12878	blood:	n/a	n/a
38	RAD21	chr19:18512526-18512825	HepG2	liver:	n/a	n/a
39	SPI1	chr19:18512443-18513166	HL-60	blood:	n/a	chr19:18512837-18512850 chr19:18512839-18512848 chr19:18512836-18512849
40	FOXM1	chr19:18512451-18512926	GM12878	blood:	n/a	n/a
41	CTCF	chr19:18512535-18512856	IMR90	lung:	n/a	n/a
42	CTCF	chr19:18512476-18512951	A549	lung:	n/a	n/a
43	MAX	chr19:18512398-18512974	A549	lung:	n/a	n/a
44	RCOR1	chr19:18512413-18512943	K562	blood:	n/a	n/a
45	RCOR1	chr19:18512521-18512721	Hela-S3	cervix:	n/a	n/a
46	PML	chr19:18512549-18512963	K562	blood:	n/a	n/a
47	MAX	chr19:18512479-18512882	MCF-7	breast:	n/a	n/a
48	CTCF	chr19:18512493-18512864	MCF-7	breast:	n/a	n/a
49	RAD21	chr19:18512532-18512769	HepG2	liver:	n/a	n/a
50	FOXA1	chr19:18512306-18512712	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18494076..18504244-chr19:18508099..18514509,16	MCF-7	breast:
2	chr19:18506537..18511375-chr19:18511397..18514824,5	K562	blood:
3	chr19:18460314..18460997-chr19:18512537..18513064,2	MCF-7	breast:
4	chr19:18390571..18392343-chr19:18511701..18513366,2	K562	blood:
5	chr19:18451491..18453396-chr19:18510638..18513266,2	K562	blood:
6	chr19:18390843..18392490-chr19:18510995..18513201,2	K562	blood:

Variant related genes	Relation type
LRRC25	TF binding region
ENSG00000130522	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000175489	Chromatin interaction
ENSG00000264175	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10421074	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10424080	0.88[ASN][1000 genomes]
rs11086108	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11671540	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12971295	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13344313	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2888142	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35336015	0.81[ASN][1000 genomes]
rs4808800	0.88[ASN][1000 genomes]
rs8112969	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749546	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
3	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
4	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911275	chr19:18484922-18586759	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
9	nsv2430	chr19:18496428-18514937	Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
10	nsv911276	chr19:18497141-18554972	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18508400-18525400	Weak transcription	Right Atrium	heart
2	chr19:18508800-18514400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:18508800-18514800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:18508800-18525200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr19:18509000-18512800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:18509000-18515200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr19:18509400-18512600	Weak transcription	Gastric	stomach
8	chr19:18510000-18512800	Weak transcription	Liver	Liver
9	chr19:18510200-18512600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:18510200-18512600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:18510200-18512800	Weak transcription	Colonic Mucosa	Colon
12	chr19:18510200-18512800	Weak transcription	Ovary	ovary
13	chr19:18510200-18512800	Weak transcription	Stomach Mucosa	stomach
14	chr19:18510400-18512600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr19:18510800-18513000	Enhancers	Hela-S3	cervix
16	chr19:18511000-18513000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:18511000-18513200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:18511400-18512600	Enhancers	Primary B cells from cord blood	blood
19	chr19:18511600-18512800	Enhancers	A549	lung
20	chr19:18511600-18513200	Enhancers	Fetal Thymus	thymus
21	chr19:18511600-18514800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr19:18511600-18515200	Enhancers	Primary hematopoietic stem cells	blood
23	chr19:18511600-18515200	Enhancers	Fetal Muscle Leg	muscle
24	chr19:18511800-18512600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr19:18511800-18512800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:18511800-18512800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:18511800-18512800	Weak transcription	NHDF-Ad	bronchial
28	chr19:18511800-18512800	Weak transcription	NHEK	skin
29	chr19:18511800-18512800	Weak transcription	NHLF	lung
30	chr19:18512000-18515800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:18512200-18512600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:18512200-18513000	Enhancers	Duodenum Mucosa	Duodenum
33	chr19:18512200-18513600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:18512200-18513600	Enhancers	K562	blood
35	chr19:18512200-18513600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr19:18512200-18514000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr19:18512200-18514000	Enhancers	Primary B cells from peripheral blood	blood
38	chr19:18512200-18514800	Enhancers	Fetal Muscle Trunk	muscle
39	chr19:18512200-18515000	Enhancers	Placenta	Placenta
40	chr19:18512200-18515200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr19:18512400-18512600	Enhancers	Lung	lung
42	chr19:18512400-18512600	Enhancers	Spleen	Spleen
43	chr19:18512400-18512600	Enhancers	HepG2	liver
44	chr19:18512400-18512800	Enhancers	Fetal Intestine Large	intestine
45	chr19:18512400-18512800	Enhancers	Fetal Intestine Small	intestine
46	chr19:18512400-18512800	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr19:18512400-18512800	Flanking Active TSS	GM12878-XiMat	blood
48	chr19:18512400-18513000	Enhancers	Dnd41	blood
49	chr19:18512400-18515000	Enhancers	Rectal Mucosa Donor 31	rectum

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