Variant report

Variant	rs12985162
Chromosome Location	chr19:41831507-41831508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41828482..41836150-chr19:41836490..41842395,12	K562	blood:
2	chr19:41811198..41813629-chr19:41830281..41833026,2	K562	blood:
3	chr19:41830987..41833840-chr19:41863132..41865918,2	MCF-7	breast:
4	chr19:41831305..41834013-chr19:41846583..41848219,2	MCF-7	breast:
5	chr19:41710873..41712522-chr19:41830997..41833166,2	K562	blood:
6	chr19:41771700..41774253-chr19:41830913..41833263,2	K562	blood:
7	chr19:41831346..41834829-chr19:41839847..41842634,3	MCF-7	breast:
8	chr19:41831307..41833980-chr19:41944294..41947067,2	MCF-7	breast:
9	chr19:41827333..41835079-chr19:41855373..41860241,10	K562	blood:
10	chr19:41825452..41832651-chr19:41855170..41863054,16	K562	blood:
11	chr19:41831464..41833596-chr19:41945378..41947616,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105329	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000105341	Chromatin interaction
ENSG00000105323	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10410836	0.83[EUR][1000 genomes]
rs10421990	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs1056854	1.00[ASW][hapmap];0.82[CEU][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11466347	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11466359	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11879429	0.83[ASN][1000 genomes]
rs11879435	0.89[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11879562	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs11880564	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11880729	0.83[ASN][1000 genomes]
rs11881940	0.82[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11881953	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12327659	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs12972266	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12972949	0.88[ASN][1000 genomes]
rs12974323	0.83[EUR][1000 genomes]
rs12974420	0.84[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12976536	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12977563	0.83[ASN][1000 genomes]
rs12980267	0.89[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12980298	0.83[EUR][1000 genomes]
rs12980480	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs12980942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12981053	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12983047	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs12983339	0.85[ASN][1000 genomes]
rs12984160	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12985339	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16958994	0.92[EUR][1000 genomes]
rs16958996	0.92[EUR][1000 genomes]
rs16958999	0.92[EUR][1000 genomes]
rs1865051	0.91[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs1865052	0.92[EUR][1000 genomes]
rs1865053	0.91[CEU][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs1946612	0.89[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1946613	0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2053086	0.84[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2241718	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241719	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241720	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2304230	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2304231	0.89[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2304232	0.89[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs34075897	0.95[EUR][1000 genomes]
rs34322801	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34945449	0.92[EUR][1000 genomes]
rs35501756	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35812313	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3745295	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs3752705	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs3760659	0.89[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs3760660	0.89[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs3816052	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs3826714	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs4456618	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs4591267	0.89[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs61459202	0.96[ASN][1000 genomes]
rs66724427	0.83[EUR][1000 genomes]
rs67511749	0.91[EUR][1000 genomes]
rs67744888	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6957	0.91[CEU][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs7245398	0.91[CEU][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs7248164	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs7250883	0.89[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7256416	0.83[EUR][1000 genomes]
rs7256856	0.83[EUR][1000 genomes]
rs7257310	0.91[CEU][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs7257742	0.95[EUR][1000 genomes]
rs7257825	0.83[EUR][1000 genomes]
rs7258749	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs8103839	0.84[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8105161	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs8105901	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8109167	0.91[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911769	chr19:41813676-41845801	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12985162	BCL3	cis	cerebellum	SCAN
rs12985162	FLT3LG	cis	cerebellum	SCAN
rs12985162	PLEKHA4	cis	cerebellum	SCAN
rs12985162	TMEM143	cis	parietal	SCAN
rs12985162	BAX	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41818200-41831600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:41818600-41854800	Strong transcription	Dnd41	blood
3	chr19:41823200-41832000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:41823400-41832200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:41824400-41834000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:41827000-41832800	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr19:41827200-41832000	Enhancers	NHDF-Ad	bronchial
8	chr19:41827400-41833000	Enhancers	Primary hematopoietic stem cells	blood
9	chr19:41827400-41833000	Genic enhancers	Fetal Thymus	thymus
10	chr19:41827600-41831800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
11	chr19:41827800-41832200	Enhancers	Stomach Mucosa	stomach
12	chr19:41828000-41832000	Enhancers	Duodenum Mucosa	Duodenum
13	chr19:41828400-41832200	Enhancers	Liver	Liver
14	chr19:41828600-41832200	Enhancers	Primary B cells from cord blood	blood
15	chr19:41828600-41834000	Enhancers	Placenta Amnion	Placenta Amnion
16	chr19:41828800-41831600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:41828800-41832400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:41828800-41834000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:41828800-41834400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:41829200-41831600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:41829200-41832200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:41829200-41835400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr19:41829400-41831600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:41829400-41831600	Enhancers	HUVEC	blood vessel
25	chr19:41829400-41832000	Enhancers	HSMMtube	muscle
26	chr19:41829600-41831800	Enhancers	Gastric	stomach
27	chr19:41829600-41832200	Weak transcription	Hela-S3	cervix
28	chr19:41829600-41833000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr19:41829800-41832000	Enhancers	Esophagus	oesophagus
30	chr19:41829800-41832200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:41830000-41831800	Enhancers	Colonic Mucosa	Colon
32	chr19:41830000-41831800	Enhancers	Lung	lung
33	chr19:41830000-41832000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:41830000-41832000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr19:41830000-41832000	Enhancers	Placenta	Placenta
36	chr19:41830000-41832200	Enhancers	GM12878-XiMat	blood
37	chr19:41830000-41832600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:41830000-41833000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr19:41830000-41833400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:41830200-41831600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr19:41830200-41832400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr19:41830200-41833200	Enhancers	HMEC	breast
43	chr19:41830400-41832000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:41830400-41832400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr19:41830400-41832400	Weak transcription	NHEK	skin
46	chr19:41830400-41834000	Enhancers	Fetal Lung	lung
47	chr19:41830600-41831600	Weak transcription	Primary T cells from cord blood	blood
48	chr19:41830600-41831600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr19:41830600-41831800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr19:41830600-41831800	Flanking Active TSS	A549	lung

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