Variant report

Variant	rs7250192
Chromosome Location	chr19:18723325-18723326
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	MAX	chr19:18723043-18723947	A549	lung:	n/a	n/a
2	MAX	chr19:18723046-18724138	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:18722600-18724393	H1-neurons	neurons:	n/a	n/a
4	MAX	chr19:18723158-18723901	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr19:18719758-18723372	HepG2	liver:	n/a	n/a
6	SUZ12	chr19:18722639-18725317	NT2-D1	testis:	n/a	n/a
7	CTBP2	chr19:18722603-18723462	H1-hESC	embryonic stem cell:	n/a	n/a
8	E2F6	chr19:18723108-18724113	H1-hESC	embryonic stem cell:	n/a	chr19:18723743-18723752 chr19:18723676-18723685 chr19:18723621-18723630 chr19:18723674-18723683
9	MAX	chr19:18723117-18724039	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAZ	chr19:18722480-18724396	IMR90	lung:	n/a	chr19:18722557-18722566 chr19:18722554-18722564 chr19:18722553-18722561 chr19:18722555-18722564 chr19:18722555-18722564 chr19:18722555-18722564
11	E2F6	chr19:18722525-18723644	H1-hESC	embryonic stem cell:	n/a	chr19:18722695-18722705 chr19:18723621-18723630
12	POLR2A	chr19:18721901-18724127	H1-neurons	neurons:	n/a	n/a
13	ZNF263	chr19:18722961-18723501	HEK293-T-REx	kidney:	n/a	chr19:18723254-18723263 chr19:18723287-18723308
14	REST	chr19:18722789-18724545	H1-neurons	neurons:	n/a	chr19:18723951-18723964 chr19:18722993-18723006 chr19:18723682-18723692
15	SIN3A	chr19:18723304-18723338	H1-hESC	embryonic stem cell:	n/a	n/a
16	ZBTB7A	chr19:18721115-18724078	ECC-1	luminal epithelium:	n/a	chr19:18722623-18722631
17	MAX	chr19:18723240-18724165	HepG2	liver:	n/a	n/a
18	MAX	chr19:18723223-18723478	K562	blood:	n/a	n/a
19	TAF1	chr19:18723021-18723947	H1-neurons	neurons:	n/a	n/a
20	JUND	chr19:18722902-18724244	SK-N-SH	brain:	n/a	chr19:18723675-18723684

No.	Distal block	Cell Line	Cell type
1	chr19:18720681..18723578-chr19:18792529..18794058,2	K562	blood:
2	chr19:18715795..18719274-chr19:18719391..18724999,7	MCF-7	breast:
3	chr19:18713204..18718867-chr19:18719015..18725496,7	MCF-7	breast:

Variant related genes	Relation type
CRLF1	TF binding region
TMEM59L	TF binding region
ENSG00000105696	Chromatin interaction
ENSG00000006016	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10409392	0.81[JPT][hapmap]
rs10415560	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1043192	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12609505	0.81[JPT][hapmap]
rs1468475	0.81[JPT][hapmap]
rs1862645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1966500	0.81[ASN][1000 genomes]
rs2057649	0.90[JPT][hapmap]
rs2074175	0.90[JPT][hapmap]
rs2079015	0.90[JPT][hapmap]
rs2238650	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283616	0.81[JPT][hapmap]
rs2302055	0.81[JPT][hapmap]
rs2314664	0.90[JPT][hapmap]
rs2314665	0.90[JPT][hapmap]
rs2314666	0.86[JPT][hapmap]
rs3170474	0.88[CEU][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs3761032	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808137	0.81[JPT][hapmap]
rs4808138	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808823	0.90[JPT][hapmap]
rs4808824	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4808835	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4808837	0.80[ASN][1000 genomes]
rs4808839	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6417264	0.88[EUR][1000 genomes]
rs6510993	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6554	0.81[JPT][hapmap]
rs709679	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7248037	0.81[ASN][1000 genomes]
rs7250623	0.84[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7252198	0.88[EUR][1000 genomes]
rs7256319	0.92[CEU][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7259557	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7648	0.81[JPT][hapmap]
rs916791	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv911287	chr19:18699333-18727913	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	nsv911288	chr19:18700047-18739497	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
10	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	nsv911291	chr19:18701499-18726856	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
12	nsv911292	chr19:18701499-18731658	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7250192	JUND	cis	Esophagus Muscularis	GTEx
rs7250192	PGLS	cis	parietal	SCAN
rs7250192	AP1M1	cis	parietal	SCAN
rs7250192	HAPLN4	cis	parietal	SCAN
rs7250192	UBA52	cis	lymphoblastoid	seeQTL
rs7250192	UNC13A	cis	parietal	SCAN
rs7250192	KIAA0892	cis	cerebellum	SCAN
rs7250192	NDUFA13	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18721000-18723600	Enhancers	Lung	lung
2	chr19:18721200-18723400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr19:18721200-18723400	Bivalent Enhancer	HUVEC	blood vessel
4	chr19:18721200-18724400	Bivalent Enhancer	Placenta	Placenta
5	chr19:18721400-18723400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:18721400-18723400	Enhancers	Pancreas	Pancrea
7	chr19:18721400-18723600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
8	chr19:18721400-18723600	Bivalent Enhancer	Fetal Thymus	thymus
9	chr19:18721400-18723600	Bivalent Enhancer	HMEC	breast
10	chr19:18721400-18724200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr19:18721600-18723600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr19:18721600-18724400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:18721600-18724600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr19:18721600-18724600	Bivalent Enhancer	Fetal Heart	heart
15	chr19:18721800-18724200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:18721800-18724200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
17	chr19:18721800-18724600	Bivalent Enhancer	Fetal Lung	lung
18	chr19:18721800-18725000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr19:18722000-18724000	Bivalent Enhancer	Liver	Liver
20	chr19:18722200-18723600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
21	chr19:18722200-18724200	Flanking Active TSS	Right Ventricle	heart
22	chr19:18722400-18723400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
23	chr19:18722400-18724600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr19:18722400-18724800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
25	chr19:18722400-18725200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
26	chr19:18722600-18723400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
27	chr19:18722600-18723400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:18722600-18723400	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
29	chr19:18722600-18723600	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:18722600-18723600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:18722600-18723600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
32	chr19:18722600-18723600	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
33	chr19:18722600-18723600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
34	chr19:18722600-18723800	Bivalent/Poised TSS	Thymus	Thymus
35	chr19:18722600-18724000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:18722600-18724000	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr19:18722600-18724000	Bivalent/Poised TSS	NH-A	brain
38	chr19:18722600-18724200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
39	chr19:18722600-18724200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
40	chr19:18722600-18724200	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr19:18722600-18724200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:18722600-18724200	Active TSS	Right Atrium	heart
43	chr19:18722600-18724200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
44	chr19:18722600-18724400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
45	chr19:18722800-18723400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
46	chr19:18722800-18723400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
47	chr19:18722800-18723400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:18722800-18723400	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
49	chr19:18722800-18723400	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
50	chr19:18722800-18723400	Bivalent Enhancer	GM12878-XiMat	blood

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