Variant report

Variant	rs3810153
Chromosome Location	chr19:42385469-42385470
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr19:42385402-42385503	K562	blood:	n/a	n/a
2	POLR2A	chr19:42384850-42385800	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:42384807-42385619	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:42385184-42385691	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:42385358-42385712	GM12878	blood:	n/a	n/a
6	CTCF	chr19:42385340-42385490	GM12865	blood:	n/a	n/a
7	EBF1	chr19:42385431-42385705	GM12878	blood:	n/a	chr19:42385567-42385578 chr19:42385588-42385599
8	POLR2A	chr19:42385048-42385838	SK-N-MC	brain:	n/a	n/a
9	FOXP2	chr19:42385255-42385512	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr19:42385303-42385708	GM12891	blood:	n/a	n/a
11	POLR2A	chr19:42385240-42385780	GM12892	blood:	n/a	n/a
12	POLR2A	chr19:42385137-42385678	SK-N-MC	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42382948..42385655-chr19:42457213..42459213,2	K562	blood:
2	chr19:42385318..42391505-chr19:42458040..42463569,9	MCF-7	breast:
3	chr19:42385266..42389164-chr19:42392215..42397025,5	MCF-7	breast:
4	chr19:42382327..42390135-chr19:42429723..42437438,12	MCF-7	breast:
5	chr19:42383909..42386502-chr19:42503408..42505677,2	K562	blood:
6	chr19:42384855..42393410-chr19:42428364..42439251,22	K562	blood:
7	chr19:42385208..42386943-chr19:42498779..42500778,2	K562	blood:
8	chr19:42385036..42390018-chr19:42460408..42463391,5	K562	blood:

No data

Variant related genes	Relation type
ARHGEF1	TF binding region
ENSG00000076928	Chromatin interaction
ENSG00000105404	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10404939	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs10405900	0.98[ASN][1000 genomes]
rs10407206	0.82[CEU][hapmap]
rs10408367	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10414823	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs10415452	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10416824	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10417985	0.89[CEU][hapmap];0.95[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10500284	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs12461099	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12461131	0.86[ASN][1000 genomes]
rs12972552	0.83[EUR][1000 genomes]
rs12976571	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs12979253	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs12984383	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1366610	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs1428922	0.98[ASN][1000 genomes]
rs1457144	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs1870092	0.82[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs2008798	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2075749	0.86[ASN][1000 genomes]
rs2075750	0.81[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap];0.89[ASN][1000 genomes]
rs2075752	0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2075754	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs2199829	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2290695	0.95[CHB][hapmap]
rs2305809	0.95[CHB][hapmap]
rs3786536	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs3786538	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs3922888	0.95[CHB][hapmap]
rs4803511	0.95[CHB][hapmap]
rs4803512	0.91[CHB][hapmap]
rs58857981	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6509002	0.87[CHB][hapmap]
rs7250787	0.86[ASN][1000 genomes]
rs7251336	0.82[CEU][hapmap]
rs7251960	0.82[CEU][hapmap]
rs7254214	0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7257666	0.87[ASN][1000 genomes]
rs7258163	0.83[ASN][1000 genomes]
rs7259596	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7259967	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs734107	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs73549152	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8102670	0.85[ASN][1000 genomes]
rs8104958	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs8106505	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs8113283	0.82[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs8113641	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs873282	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs882520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs891167	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs899662	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs930102	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats 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	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3810153	SLC1A5	cis	parietal	SCAN
rs3810153	EXOC3L2	cis	cerebellum	SCAN
rs3810153	RABAC1	Cis_1M	lymphoblastoid	RTeQTL
rs3810153	EHD2	cis	parietal	SCAN
rs3810153	LIG1	cis	parietal	SCAN
rs3810153	ZNF227	cis	cerebellum	SCAN
rs3810153	PVR	cis	parietal	SCAN
rs3810153	IGFL1	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42369600-42386400	Weak transcription	Fetal Kidney	kidney
2	chr19:42374600-42386600	Weak transcription	Right Atrium	heart
3	chr19:42375400-42386200	Weak transcription	Hela-S3	cervix
4	chr19:42376000-42386400	Weak transcription	Brain Anterior Caudate	brain
5	chr19:42376000-42386400	Weak transcription	Fetal Lung	lung
6	chr19:42376000-42386600	Weak transcription	HSMMtube	muscle
7	chr19:42376200-42386400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:42376200-42386400	Weak transcription	Psoas Muscle	Psoas
9	chr19:42376400-42386400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:42376400-42386400	Weak transcription	Brain Substantia Nigra	brain
11	chr19:42376400-42386400	Weak transcription	Colon Smooth Muscle	Colon
12	chr19:42376400-42386400	Weak transcription	Esophagus	oesophagus
13	chr19:42376400-42386400	Weak transcription	Gastric	stomach
14	chr19:42376400-42386400	Weak transcription	Left Ventricle	heart
15	chr19:42376400-42386400	Weak transcription	HMEC	breast
16	chr19:42376400-42386400	Weak transcription	HUVEC	blood vessel
17	chr19:42376600-42386400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr19:42376600-42386400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:42376600-42386400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr19:42376600-42386400	Weak transcription	Lung	lung
21	chr19:42376600-42386600	Weak transcription	NHDF-Ad	bronchial
22	chr19:42376800-42386200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:42376800-42386400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:42376800-42386600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:42377200-42386400	Weak transcription	Brain Angular Gyrus	brain
26	chr19:42377200-42386600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:42377200-42386800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr19:42377400-42386400	Weak transcription	Pancreas	Pancrea
29	chr19:42377400-42386400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr19:42377400-42386400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr19:42377600-42386400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr19:42380200-42386400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr19:42381000-42386400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:42381600-42386200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:42381600-42386400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:42382200-42386200	Enhancers	Primary T cells fromperipheralblood	blood
37	chr19:42382200-42386200	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr19:42382400-42386000	Enhancers	Primary T cells from cord blood	blood
39	chr19:42382400-42386200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr19:42382400-42386200	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr19:42382400-42386200	Weak transcription	A549	lung
42	chr19:42382400-42386400	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr19:42382400-42386400	Weak transcription	Adipose Nuclei	Adipose
44	chr19:42382600-42385600	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr19:42382600-42386200	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr19:42382600-42386400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr19:42382600-42386400	Weak transcription	Colonic Mucosa	Colon
48	chr19:42382600-42386400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr19:42382800-42386400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:42383200-42386200	Enhancers	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links