Variant report

Variant	rs3816052
Chromosome Location	chr19:41773797-41773798
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	WRNIP1	chr19:41773788-41773923	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:41773734-41773799	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr19:41767879-41773979	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:41773510-41773820	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:41773704-41774323	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:41772492-41774260	IMR90	lung:	n/a	n/a
7	EBF1	chr19:41773470-41773825	GM12878	blood:	n/a	chr19:41773625-41773636
8	POLR2A	chr19:41772387-41773956	GM12892	blood:	n/a	n/a
9	POLR2A	chr19:41772654-41774367	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:41772332-41774072	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr19:41773639-41773873	GM12891	blood:	n/a	n/a
12	FOS	chr19:41773750-41773800	MCF10A-Er-Src	breast:	n/a	chr19:41773782-41773792 chr19:41773783-41773791 chr19:41773784-41773791 chr19:41773782-41773792 chr19:41773783-41773791 chr19:41773782-41773792
13	POLR2A	chr19:41772250-41773848	GM12892	blood:	n/a	n/a
14	CHD1	chr19:41767372-41774470	IMR90	lung:	n/a	chr19:41770254-41770264 chr19:41768452-41768462
15	POLR2A	chr19:41772318-41774556	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:41767921-41774352	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41773353..41775268-chr19:41816276..41817843,2	K562	blood:
2	chr19:41773179..41775714-chr19:41780883..41782386,2	MCF-7	breast:

Variant related genes	Relation type
HNRNPUL1	TF binding region
ENSG00000142039	Chromatin interaction
ENSG00000105323	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10410836	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421990	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1056854	1.00[CEU][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs11466359	0.86[EUR][1000 genomes]
rs11879429	0.81[EUR][1000 genomes]
rs11879435	0.81[EUR][1000 genomes]
rs11879562	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11880564	0.86[EUR][1000 genomes]
rs11880729	0.80[EUR][1000 genomes]
rs11881940	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11881953	0.94[EUR][1000 genomes]
rs11882467	0.95[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs12327659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12462203	0.90[CHB][hapmap]
rs12972266	0.92[EUR][1000 genomes]
rs12972949	0.85[EUR][1000 genomes]
rs12974323	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12974420	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs12975585	0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs12975920	0.98[ASN][1000 genomes]
rs12976536	0.98[EUR][1000 genomes]
rs12977563	0.81[EUR][1000 genomes]
rs12978323	0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs12980298	0.96[ASN][1000 genomes]
rs12980480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12980839	0.91[ASN][1000 genomes]
rs12980942	0.85[CEU][hapmap]
rs12983047	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.96[ASN][1000 genomes]
rs12984160	0.91[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs12985162	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs12985339	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs13345456	0.97[ASN][1000 genomes]
rs16958994	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16958996	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16958999	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1865051	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1865052	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1865053	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1946613	0.84[EUR][1000 genomes]
rs2053086	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs2241718	0.91[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs2241719	0.86[EUR][1000 genomes]
rs2241720	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2304230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304231	0.84[EUR][1000 genomes]
rs2304232	0.84[EUR][1000 genomes]
rs2304234	0.90[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs34075897	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34322801	0.88[EUR][1000 genomes]
rs34945449	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35501756	0.89[EUR][1000 genomes]
rs35812313	0.98[EUR][1000 genomes]
rs3745295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760660	0.84[EUR][1000 genomes]
rs3786555	0.83[ASN][1000 genomes]
rs3826714	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4456618	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4591267	0.84[EUR][1000 genomes]
rs4802111	0.90[CHB][hapmap]
rs4802112	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs4802113	0.89[CHB][hapmap]
rs4802115	0.81[ASN][1000 genomes]
rs4803448	0.90[CHB][hapmap]
rs4803449	0.90[CHB][hapmap]
rs6508974	0.90[CHB][hapmap]
rs66724427	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67511749	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67744888	0.98[EUR][1000 genomes]
rs6957	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7245398	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7246525	0.90[CHB][hapmap]
rs7248164	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7254679	0.91[ASN][1000 genomes]
rs7256416	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256856	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257310	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7257742	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7257825	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7258749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8103839	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs8105161	0.91[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.91[ASN][1000 genomes]
rs8105901	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs8109167	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109627	0.95[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][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	esv17637	chr19:41770228-41815282	Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3816052	BAX	cis	cerebellum	SCAN
rs3816052	PLEKHA4	cis	cerebellum	SCAN
rs3816052	TSKS	cis	parietal	SCAN
rs3816052	FLT3LG	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41772000-41774600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41772200-41773800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:41772200-41773800	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr19:41772200-41773800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr19:41772200-41774200	Enhancers	Stomach Mucosa	stomach
6	chr19:41772200-41774800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:41772400-41773800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:41772400-41773800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:41772400-41773800	Genic enhancers	Fetal Stomach	stomach
10	chr19:41772400-41774000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr19:41772600-41773800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr19:41772600-41773800	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr19:41772600-41773800	Enhancers	Fetal Heart	heart
14	chr19:41772600-41773800	Genic enhancers	Fetal Lung	lung
15	chr19:41772600-41773800	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr19:41772600-41773800	Enhancers	Right Ventricle	heart
17	chr19:41772600-41773800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr19:41772600-41774000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr19:41772600-41774000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr19:41772600-41774000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr19:41772600-41774000	Enhancers	Colon Smooth Muscle	Colon
22	chr19:41772600-41774200	Genic enhancers	Fetal Muscle Leg	muscle
23	chr19:41772600-41774400	Genic enhancers	Primary T cells fromperipheralblood	blood
24	chr19:41772800-41773800	Genic enhancers	Primary B cells from cord blood	blood
25	chr19:41772800-41773800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr19:41772800-41773800	Genic enhancers	Brain Angular Gyrus	brain
27	chr19:41772800-41773800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr19:41772800-41773800	Genic enhancers	Fetal Intestine Large	intestine
29	chr19:41772800-41774000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
30	chr19:41772800-41774200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr19:41772800-41774200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
32	chr19:41772800-41794400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr19:41773000-41773800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:41773000-41773800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:41773000-41773800	Genic enhancers	Muscle Satellite Cultured Cells	--
36	chr19:41773000-41773800	Genic enhancers	Brain Hippocampus Middle	brain
37	chr19:41773000-41773800	Genic enhancers	Fetal Thymus	thymus
38	chr19:41773000-41773800	Genic enhancers	Rectal Mucosa Donor 29	rectum
39	chr19:41773000-41773800	Transcr. at gene 5' and 3'	Hela-S3	cervix
40	chr19:41773000-41773800	Genic enhancers	HepG2	liver
41	chr19:41773000-41774200	Weak transcription	HSMMtube	muscle
42	chr19:41773000-41774400	Weak transcription	Fetal Brain Male	brain
43	chr19:41773000-41776800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr19:41773000-41777400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr19:41773000-41802400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:41773000-41804000	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr19:41773200-41773800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr19:41773200-41773800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:41773200-41773800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
50	chr19:41773200-41773800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links