Variant report

Variant	rs8109167
Chromosome Location	chr19:41823167-41823168
allele	G/T
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:2)
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	POLR2A	chr19:41822866-41823411	U87	brain:	n/a	n/a
2	POLR2A	chr19:41822247-41823455	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr19:41821741-41823319	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr19:41821742-41835294	K562	blood:	n/a	n/a
5	POLR2A	chr19:41823157-41823517	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:41822766-41823173	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:41822890-41823413	U87	brain:	n/a	n/a
8	POLR2A	chr19:41821510-41835091	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr19:41821607-41823649	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:41822119-41823194	K562	blood:	n/a	n/a
11	POLR2A	chr19:41821964-41823427	U87	brain:	n/a	n/a
12	POLR2A	chr19:41821697-41823396	HUVEC	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41821189..41824039-chr19:41826906..41830511,3	MCF-7	breast:
2	chr19:41821413..41824175-chr19:41850214..41852435,2	MCF-7	breast:

No data

Variant related genes	Relation type
CCDC97	TF binding region
ENSG00000105329	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	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10421990	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];0.85[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];0.88[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]
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];0.91[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.85[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	0.91[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];0.80[CHD][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	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12980480	0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.91[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	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958996	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958999	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865051	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]
rs1865052	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865053	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];1.00[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];0.91[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304234	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs34075897	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34322801	0.96[EUR][1000 genomes]
rs34945449	0.91[AFR][1000 genomes];1.00[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];0.88[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3752705	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3816052	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]
rs3826714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.98[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];0.81[YRI][hapmap];0.98[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	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67511749	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67744888	0.89[EUR][1000 genomes]
rs6957	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7245398	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.93[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];0.91[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7254679	0.82[CEU][hapmap];0.92[ASN][1000 genomes]
rs7256416	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7256856	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7257310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257742	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257825	0.83[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];0.84[YRI][hapmap];0.91[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];0.86[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8105901	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs8109627	1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][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
rs8109167	TSKS	cis	parietal	SCAN
rs8109167	FLT3LG	cis	cerebellum	SCAN
rs8109167	PLEKHA4	cis	cerebellum	SCAN
rs8109167	BAX	cis	cerebellum	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	chr19:41818200-41824600	Strong transcription	Spleen	Spleen
14	chr19:41818200-41825600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:41818200-41825800	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr19:41818200-41825800	Strong transcription	A549	lung
17	chr19:41818200-41826800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:41818200-41826800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:41818200-41827200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr19:41818200-41827200	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr19:41818200-41827400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:41818200-41827400	Strong transcription	Osteobl	bone
23	chr19:41818200-41827600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:41818200-41828400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr19:41818200-41831600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:41818400-41823200	Strong transcription	Esophagus	oesophagus
27	chr19:41818400-41824400	Strong transcription	Placenta	Placenta
28	chr19:41818400-41824600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:41818400-41825400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr19:41818400-41827000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:41818400-41827200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:41818400-41827200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr19:41818400-41827400	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr19:41818400-41827400	Strong transcription	Fetal Thymus	thymus
35	chr19:41818400-41829000	Strong transcription	Fetal Intestine Large	intestine
36	chr19:41818400-41831200	Strong transcription	Thymus	Thymus
37	chr19:41818600-41823600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:41818600-41825800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:41818600-41826200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr19:41818600-41826400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:41818600-41827200	Strong transcription	Lung	lung
42	chr19:41818600-41854800	Strong transcription	Dnd41	blood
43	chr19:41818800-41823600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:41818800-41825600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr19:41818800-41827000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:41819000-41827000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr19:41819000-41827200	Strong transcription	Adipose Nuclei	Adipose
48	chr19:41819000-41827400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr19:41819000-41827800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:41819000-41830600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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