Variant report

Variant	rs11879562
Chromosome Location	chr19:41804976-41804977
allele	C/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:4)
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	chr19:41802941-41805120	IMR90	lung:	n/a	n/a
2	POLR2A	chr19:41802916-41805887	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr19:41804967-41805367	K562	blood:	n/a	n/a
4	POLR2A	chr19:41804122-41806294	U87	brain:	n/a	n/a
5	POLR2A	chr19:41803411-41805383	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:41802778-41805200	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:41804948-41805301	GM12891	blood:	n/a	n/a
8	POLR2A	chr19:41804880-41805263	K562	blood:	n/a	n/a
9	POLR2A	chr19:41802024-41805328	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:41802723-41805323	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:41804616-41805171	K562	blood:	n/a	n/a
12	POLR2A	chr19:41801390-41806787	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41769310..41770884-chr19:41804144..41807027,2	MCF-7	breast:
2	chr19:41799355..41806261-chr19:41812914..41817863,9	MCF-7	breast:
3	chr19:41800013..41801896-chr19:41804491..41806088,2	K562	blood:
4	chr19:41804854..41807401-chr19:41811549..41813471,2	K562	blood:

No data

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

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10410836	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10421990	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056854	1.00[CEU][hapmap];0.89[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]
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]
rs12327659	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462203	0.90[CHB][hapmap]
rs12972266	0.92[EUR][1000 genomes]
rs12972949	0.85[EUR][1000 genomes]
rs12974323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12974420	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs12975585	0.95[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.93[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];0.80[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs12980298	0.99[ASN][1000 genomes]
rs12980480	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12980839	0.94[ASN][1000 genomes]
rs12980942	0.85[CEU][hapmap]
rs12983047	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12984160	0.91[CEU][hapmap];0.89[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	1.00[ASN][1000 genomes]
rs16958994	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16958996	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16958999	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16975124	0.84[LWK][hapmap]
rs16975164	0.84[LWK][hapmap]
rs1865051	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1865052	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1865053	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304231	0.84[EUR][1000 genomes]
rs2304232	0.84[EUR][1000 genomes]
rs2304234	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs34075897	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34322801	0.88[EUR][1000 genomes]
rs34945449	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35501756	0.89[EUR][1000 genomes]
rs35812313	0.98[EUR][1000 genomes]
rs3745295	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3752705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760660	0.84[EUR][1000 genomes]
rs3786555	0.81[ASN][1000 genomes]
rs3816052	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]
rs3826714	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4456618	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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]
rs4803448	0.90[CHB][hapmap]
rs4803449	0.90[CHB][hapmap]
rs6508974	0.90[CHB][hapmap]
rs66724427	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67511749	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67744888	0.98[EUR][1000 genomes]
rs6957	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7245398	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246525	0.90[CHB][hapmap]
rs7248164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];1.00[ASN][1000 genomes]
rs7254679	0.94[ASN][1000 genomes]
rs7256416	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7256856	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7257310	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7257742	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7257825	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103839	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs8105161	0.80[ASW][hapmap];0.91[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.88[YRI][hapmap];0.94[ASN][1000 genomes]
rs8105901	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs8109167	0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8109627	0.95[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.97[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
rs11879562	BAX	cis	cerebellum	SCAN
rs11879562	PLEKHA4	cis	cerebellum	SCAN
rs11879562	FLT3LG	cis	cerebellum	SCAN
rs11879562	TSKS	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41773200-41814400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41773600-41812600	Strong transcription	A549	lung
3	chr19:41773800-41814200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:41773800-41814200	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr19:41773800-41814200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr19:41774000-41812600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:41774000-41814200	Strong transcription	Fetal Brain Female	brain
8	chr19:41774400-41807600	Strong transcription	Dnd41	blood
9	chr19:41780200-41815800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr19:41780600-41812000	Strong transcription	HUVEC	blood vessel
11	chr19:41782800-41808200	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr19:41783800-41814400	Strong transcription	Brain Germinal Matrix	brain
13	chr19:41788600-41815400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr19:41794200-41813800	Strong transcription	K562	blood
15	chr19:41794400-41805000	Strong transcription	Fetal Kidney	kidney
16	chr19:41795200-41814000	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr19:41795400-41812400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
18	chr19:41795400-41813800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr19:41795400-41814200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr19:41795600-41812800	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr19:41795600-41812800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:41795600-41813200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:41795600-41813800	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr19:41795600-41813800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr19:41795600-41814200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:41796400-41812800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:41797400-41812600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:41800000-41805200	Genic enhancers	Gastric	stomach
29	chr19:41800000-41806600	Genic enhancers	Stomach Mucosa	stomach
30	chr19:41800000-41806800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:41800000-41808800	Genic enhancers	Duodenum Mucosa	Duodenum
32	chr19:41800200-41805400	Genic enhancers	Fetal Intestine Large	intestine
33	chr19:41800200-41805600	Genic enhancers	Fetal Intestine Small	intestine
34	chr19:41800200-41806800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr19:41801400-41805200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:41801400-41806200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr19:41801400-41807800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr19:41801600-41806800	Genic enhancers	Left Ventricle	heart
39	chr19:41801600-41807800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr19:41801600-41808400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
41	chr19:41801600-41808800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:41801600-41808800	Genic enhancers	Fetal Muscle Leg	muscle
43	chr19:41801600-41813200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:41801600-41814600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:41801800-41808400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
46	chr19:41801800-41811600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr19:41802000-41806000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr19:41802000-41806200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:41802000-41808600	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr19:41802200-41805000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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