Variant report

Variant	rs12327659
Chromosome Location	chr19:41796472-41796473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41796248-41796524	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr19:41796375-41796575	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:41796366-41796495	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:41796319-41796503	K562	blood:	n/a	n/a
5	POLR2A	chr19:41796264-41796490	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41795143..41797653-chr19:41797943..41800944,4	MCF-7	breast:
2	chr19:41795917..41800986-chr19:41806343..41812071,5	K562	blood:
3	chr19:41795075..41798601-chr19:41814323..41817151,3	K562	blood:
4	chr19:41795110..41797516-chr19:41801008..41803885,2	MCF-7	breast:
5	chr19:41782120..41784919-chr19:41794463..41796604,3	K562	blood:

No data

Variant related genes	Relation type
RN7SL34P	TF binding region
ENSG00000105323	Chromatin interaction
ENSG00000142039	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10410836	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10421990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.97[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]
rs11879562	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]
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]
rs12462203	0.90[CHB][hapmap]
rs12972266	0.92[EUR][1000 genomes]
rs12972949	0.85[EUR][1000 genomes]
rs12974323	0.87[AFR][1000 genomes];0.94[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];0.94[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];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs12980298	0.99[ASN][1000 genomes]
rs12980480	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.94[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	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.83[YRI][hapmap];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	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16958996	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16958999	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16975124	0.80[LWK][hapmap]
rs16975164	0.80[LWK][hapmap]
rs1865051	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]
rs1865052	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1865053	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.85[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	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[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	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34322801	0.88[EUR][1000 genomes]
rs34945449	0.85[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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3752705	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[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];0.88[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]
rs3826714	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.86[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];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67511749	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67744888	0.98[EUR][1000 genomes]
rs6957	0.86[ASW][hapmap];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[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7245398	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246525	0.90[CHB][hapmap]
rs7248164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254679	0.94[ASN][1000 genomes]
rs7256416	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7256856	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7257310	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7257742	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7257825	0.84[AFR][1000 genomes];0.98[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];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[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	0.86[ASW][hapmap];0.91[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.83[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];0.91[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]
rs8109627	0.95[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs998468	0.83[LWK][hapmap]

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
rs12327659	TSKS	cis	parietal	SCAN
rs12327659	BAX	cis	cerebellum	SCAN
rs12327659	FLT3LG	cis	cerebellum	SCAN
rs12327659	PLEKHA4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41773000-41802400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:41773000-41804000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr19:41773200-41802200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:41773200-41814400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:41773400-41802200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr19:41773400-41802200	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr19:41773600-41801400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr19:41773600-41801800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:41773600-41802200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr19:41773600-41802200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:41773600-41802200	Strong transcription	Placenta	Placenta
12	chr19:41773600-41802200	Strong transcription	HSMM	muscle
13	chr19:41773600-41802800	Weak transcription	Right Atrium	heart
14	chr19:41773600-41803400	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr19:41773600-41804400	Strong transcription	Thymus	Thymus
16	chr19:41773600-41812600	Strong transcription	A549	lung
17	chr19:41773800-41798400	Strong transcription	Adipose Nuclei	Adipose
18	chr19:41773800-41800200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr19:41773800-41800200	Strong transcription	Fetal Intestine Large	intestine
20	chr19:41773800-41800200	Strong transcription	Fetal Intestine Small	intestine
21	chr19:41773800-41801400	Strong transcription	HMEC	breast
22	chr19:41773800-41801600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:41773800-41801600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:41773800-41801600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:41773800-41802000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr19:41773800-41802200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr19:41773800-41802200	Strong transcription	Fetal Thymus	thymus
28	chr19:41773800-41802200	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr19:41773800-41802400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:41773800-41802600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr19:41773800-41802800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:41773800-41802800	Strong transcription	Fetal Stomach	stomach
33	chr19:41773800-41803200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:41773800-41803800	Strong transcription	Liver	Liver
35	chr19:41773800-41814200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:41773800-41814200	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:41773800-41814200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:41774000-41800000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr19:41774000-41800400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:41774000-41801000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:41774000-41801400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:41774000-41802000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:41774000-41802200	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr19:41774000-41802600	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr19:41774000-41812600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr19:41774000-41814200	Strong transcription	Fetal Brain Female	brain
47	chr19:41774200-41801600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr19:41774200-41801600	Strong transcription	Fetal Muscle Leg	muscle
49	chr19:41774200-41801800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr19:41774200-41802200	Strong transcription	Stomach Smooth Muscle	stomach

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