Variant report

Variant	rs1865051
Chromosome Location	chr19:41824885-41824886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:69)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:69 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41824458-41826474	GM18951	blood:	n/a	n/a
2	NFATC1	chr19:41824832-41825694	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:41824254-41832602	PFSK-1	brain:	n/a	n/a
4	MTA3	chr19:41824327-41825120	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:41824286-41831523	K562	blood:	n/a	n/a
6	POLR2A	chr19:41824431-41828048	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:41824337-41828000	HL-60	blood:	n/a	n/a
8	POLR2A	chr19:41824877-41824990	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr19:41823962-41834762	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr19:41824178-41828317	GM12892	blood:	n/a	n/a
11	POLR2A	chr19:41824436-41826911	GM12878	blood:	n/a	n/a
12	PBX3	chr19:41824341-41828224	A549	lung:	n/a	chr19:41824565-41824574
13	POLR2A	chr19:41824584-41826068	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr19:41824387-41825464	A549	lung:	n/a	n/a
15	POLR2A	chr19:41823290-41832793	HepG2	liver:	n/a	n/a
16	POLR2A	chr19:41824224-41825566	U87	brain:	n/a	n/a
17	POLR2A	chr19:41824341-41825509	HUVEC	blood vessel:	n/a	n/a
18	BCL3	chr19:41824632-41828077	A549	lung:	n/a	n/a
19	POLR2A	chr19:41824201-41828069	U87	brain:	n/a	n/a
20	POLR2A	chr19:41824355-41828205	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr19:41824218-41825480	U87	brain:	n/a	n/a
22	POLR2A	chr19:41824262-41831629	GM12892	blood:	n/a	n/a
23	POLR2A	chr19:41824378-41828028	HepG2	liver:	n/a	n/a
24	POLR2A	chr19:41824687-41825082	A549	lung:	n/a	n/a
25	POLR2A	chr19:41824880-41825135	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr19:41824422-41825412	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr19:41824629-41826497	A549	lung:	n/a	n/a
28	POLR2A	chr19:41824190-41828239	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr19:41824200-41828041	GM12892	blood:	n/a	n/a
30	POLR2A	chr19:41824400-41827933	GM19193	blood:	n/a	n/a
31	POLR2A	chr19:41824656-41825135	HepG2	liver:	n/a	n/a
32	POLR2A	chr19:41821742-41835294	K562	blood:	n/a	n/a
33	FOXA2	chr19:41824630-41825295	A549	lung:	n/a	n/a
34	POLR2A	chr19:41824269-41827950	GM12891	blood:	n/a	n/a
35	POLR2A	chr19:41824496-41827951	GM12892	blood:	n/a	n/a
36	POLR2A	chr19:41824710-41825073	HepG2	liver:	n/a	n/a
37	POLR2A	chr19:41824598-41828109	PANC-1	pancreas:	n/a	n/a
38	POLR2A	chr19:41824402-41825499	K562	blood:	n/a	n/a
39	POLR2A	chr19:41824707-41825085	A549	lung:	n/a	n/a
40	POLR2A	chr19:41824732-41825418	K562	blood:	n/a	n/a
41	POLR2A	chr19:41824253-41835104	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr19:41824685-41825251	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr19:41824585-41825097	A549	lung:	n/a	n/a
44	POLR2A	chr19:41821510-41835091	SK-N-MC	brain:	n/a	n/a
45	POLR2A	chr19:41824669-41824911	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr19:41824404-41826731	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr19:41824656-41825476	GM12878	blood:	n/a	n/a
48	BCL3	chr19:41824372-41832690	A549	lung:	n/a	chr19:41831877-41831890 chr19:41831853-41831862
49	POLR2A	chr19:41824127-41831561	GM12878	blood:	n/a	n/a
50	POLR2A	chr19:41824204-41825548	GM12892	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41813982..41818537-chr19:41824784..41829010,7	MCF-7	breast:
2	chr19:41769787..41771602-chr19:41823393..41825966,2	MCF-7	breast:
3	chr19:41824554..41827469-chr19:41868894..41871689,2	K562	blood:

No data

Variant related genes	Relation type
CCDC97	TF binding region
ENSG00000105323	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000142039	Chromatin interaction
ENSG00000123810	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10410836	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10421990	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1056854	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs11466359	0.95[EUR][1000 genomes]
rs11879562	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]
rs11880564	0.95[EUR][1000 genomes]
rs11881940	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs11881953	0.86[EUR][1000 genomes]
rs11882467	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12327659	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12462203	0.85[CHB][hapmap]
rs12972266	0.95[EUR][1000 genomes]
rs12974323	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12974420	0.91[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs12975585	0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs12975920	0.95[ASN][1000 genomes]
rs12976536	0.89[EUR][1000 genomes]
rs12978323	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs12980298	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12980480	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]
rs12980839	0.92[ASN][1000 genomes]
rs12980942	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12981053	0.82[EUR][1000 genomes]
rs12983047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12984160	1.00[CEU][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs12985162	0.91[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs12985339	0.91[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs13345456	0.97[ASN][1000 genomes]
rs16958994	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958996	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958999	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865052	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865053	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053086	0.91[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs2241718	1.00[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs2241719	0.95[EUR][1000 genomes]
rs2241720	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2304230	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];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304234	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs34075897	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34322801	0.96[EUR][1000 genomes]
rs34945449	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35501756	0.98[EUR][1000 genomes]
rs35812313	0.89[EUR][1000 genomes]
rs3745295	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3752705	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3816052	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]
rs3826714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456618	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802111	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs4802112	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4802113	0.84[CHB][hapmap]
rs4803448	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs4803449	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs6508974	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs66724427	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67511749	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67744888	0.89[EUR][1000 genomes]
rs6957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7245398	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7246525	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs7248164	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7254679	0.82[CEU][hapmap];0.92[ASN][1000 genomes]
rs7256416	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7256856	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7257310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257742	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257825	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7258749	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8103839	0.91[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs8105161	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8105901	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs8109167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109627	0.89[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.81[MKK][hapmap];1.00[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1865051	BAX	cis	cerebellum	SCAN
rs1865051	PLEKHA4	cis	cerebellum	SCAN
rs1865051	FLT3LG	cis	cerebellum	SCAN
rs1865051	TSKS	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41817000-41827800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41817200-41827200	Weak transcription	Right Atrium	heart
3	chr19:41817400-41825200	Weak transcription	Stomach Mucosa	stomach
4	chr19:41817600-41827600	Strong transcription	Fetal Stomach	stomach
5	chr19:41817800-41827000	Strong transcription	Fetal Muscle Leg	muscle
6	chr19:41817800-41827200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:41817800-41828800	Strong transcription	Fetal Intestine Small	intestine
8	chr19:41817800-41829200	Weak transcription	Fetal Brain Male	brain
9	chr19:41818000-41825400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:41818000-41827200	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr19:41818000-41828800	Weak transcription	Hela-S3	cervix
12	chr19:41818000-41829000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:41818200-41825600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr19:41818200-41825800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr19:41818200-41825800	Strong transcription	A549	lung
16	chr19:41818200-41826800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:41818200-41826800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:41818200-41827200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:41818200-41827200	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr19:41818200-41827400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:41818200-41827400	Strong transcription	Osteobl	bone
22	chr19:41818200-41827600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:41818200-41828400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr19:41818200-41831600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:41818400-41825400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:41818400-41827000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr19:41818400-41827200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:41818400-41827200	Strong transcription	Stomach Smooth Muscle	stomach
29	chr19:41818400-41827400	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr19:41818400-41827400	Strong transcription	Fetal Thymus	thymus
31	chr19:41818400-41829000	Strong transcription	Fetal Intestine Large	intestine
32	chr19:41818400-41831200	Strong transcription	Thymus	Thymus
33	chr19:41818600-41825800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:41818600-41826200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr19:41818600-41826400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:41818600-41827200	Strong transcription	Lung	lung
37	chr19:41818600-41854800	Strong transcription	Dnd41	blood
38	chr19:41818800-41825600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:41818800-41827000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:41819000-41827000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr19:41819000-41827200	Strong transcription	Adipose Nuclei	Adipose
42	chr19:41819000-41827400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr19:41819000-41827800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:41819000-41830600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr19:41819200-41829200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr19:41819400-41827600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr19:41819600-41827000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr19:41819600-41828600	Weak transcription	Small Intestine	intestine
49	chr19:41819600-41829000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr19:41819800-41827400	Strong transcription	Primary B cells from peripheral blood	blood

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