Variant report

Variant	rs8103839
Chromosome Location	chr19:41781493-41781494
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41780528-41781736	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:41781345-41781712	K562	blood:	n/a	n/a
3	POLR2A	chr19:41781284-41781779	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:41781398-41781555	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:41781348-41781794	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:41781147-41781757	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:41781383-41781739	K562	blood:	n/a	n/a
8	POLR2A	chr19:41779482-41781838	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:41781419-41781662	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:41781186-41781842	GM12892	blood:	n/a	n/a
11	POLR2A	chr19:41781458-41781655	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr19:41781289-41781493	K562	blood:	n/a	n/a
13	POLR2A	chr19:41780645-41781877	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr19:41780645-41781845	GM12892	blood:	n/a	n/a
15	POLR2A	chr19:41781405-41781800	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr19:41780459-41781669	K562	blood:	n/a	n/a
17	POLR2A	chr19:41781473-41781789	K562	blood:	n/a	n/a
18	POLR2A	chr19:41781447-41781779	K562	blood:	n/a	n/a
19	POLR2A	chr19:41781228-41781627	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41773179..41775714-chr19:41780883..41782386,2	MCF-7	breast:
2	chr19:41770083..41771772-chr19:41780839..41782366,2	MCF-7	breast:

No data

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

Extended variants
information (count: 84 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10410836	0.98[EUR][1000 genomes]
rs10421990	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs1056854	0.84[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11466345	0.81[JPT][hapmap]
rs11466347	0.84[ASN][1000 genomes]
rs11466359	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11879429	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11879435	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11879562	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs11880564	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11880729	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11881940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11881953	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12327659	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs12972266	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12972779	0.83[ASN][1000 genomes]
rs12972949	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12974323	0.98[EUR][1000 genomes]
rs12974420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12976536	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12977563	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12980267	0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12980480	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs12980942	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12981053	0.91[ASN][1000 genomes]
rs12982872	0.84[ASN][1000 genomes]
rs12983027	0.84[ASN][1000 genomes]
rs12983047	0.91[CEU][hapmap]
rs12983339	0.96[ASN][1000 genomes]
rs12984160	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12985162	0.84[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12985339	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16958994	0.89[EUR][1000 genomes]
rs16958996	0.89[EUR][1000 genomes]
rs16958999	0.89[EUR][1000 genomes]
rs1865051	0.91[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs1865052	0.89[EUR][1000 genomes]
rs1865053	0.91[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs1946612	0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs1946613	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053086	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241718	0.84[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2241719	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2241720	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2304230	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs2304231	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304232	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304235	0.83[ASN][1000 genomes]
rs34075897	0.86[EUR][1000 genomes]
rs34322801	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34772093	0.88[ASN][1000 genomes]
rs34945449	0.89[EUR][1000 genomes]
rs35310790	0.82[ASN][1000 genomes]
rs35501756	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35546772	0.89[ASN][1000 genomes]
rs35812313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3745295	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs3752705	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs3760659	0.94[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs3760660	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3786556	0.83[ASN][1000 genomes]
rs3816052	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs3826714	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs4456618	0.91[CEU][hapmap];0.80[CHB][hapmap];0.92[EUR][1000 genomes]
rs4591267	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61459202	0.91[ASN][1000 genomes]
rs66724427	0.98[EUR][1000 genomes]
rs67511749	0.89[EUR][1000 genomes]
rs67744888	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6957	0.91[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs7245398	0.91[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs7248164	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs7250883	0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs7256416	0.98[EUR][1000 genomes]
rs7256856	0.98[EUR][1000 genomes]
rs7256873	0.82[ASN][1000 genomes]
rs7257310	0.91[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs7257742	0.86[EUR][1000 genomes]
rs7257825	0.98[EUR][1000 genomes]
rs7258749	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs8105161	0.91[CEU][hapmap]
rs8105901	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];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8109167	0.91[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][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
rs8103839	BAX	cis	cerebellum	SCAN
rs8103839	TSKS	cis	parietal	SCAN
rs8103839	FLT3LG	cis	cerebellum	SCAN
rs8103839	PLEKHA4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41772800-41794400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
2	chr19:41773000-41802400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:41773000-41804000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr19:41773200-41794400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr19:41773200-41794600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr19:41773200-41802200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:41773200-41814400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:41773400-41783000	Strong transcription	Fetal Kidney	kidney
9	chr19:41773400-41788000	Strong transcription	Brain Cingulate Gyrus	brain
10	chr19:41773400-41788400	Strong transcription	Primary hematopoietic stem cells	blood
11	chr19:41773400-41788600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:41773400-41792600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:41773400-41793200	Strong transcription	Brain Anterior Caudate	brain
14	chr19:41773400-41794400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr19:41773400-41794600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr19:41773400-41802200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr19:41773400-41802200	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr19:41773600-41788000	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr19:41773600-41788400	Strong transcription	Esophagus	oesophagus
20	chr19:41773600-41792600	Strong transcription	Rectal Smooth Muscle	rectum
21	chr19:41773600-41792800	Strong transcription	Colonic Mucosa	Colon
22	chr19:41773600-41793400	Strong transcription	K562	blood
23	chr19:41773600-41793400	Strong transcription	NH-A	brain
24	chr19:41773600-41793600	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr19:41773600-41801400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:41773600-41801800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:41773600-41802200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr19:41773600-41802200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:41773600-41802200	Strong transcription	Placenta	Placenta
30	chr19:41773600-41802200	Strong transcription	HSMM	muscle
31	chr19:41773600-41802800	Weak transcription	Right Atrium	heart
32	chr19:41773600-41803400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr19:41773600-41804400	Strong transcription	Thymus	Thymus
34	chr19:41773600-41812600	Strong transcription	A549	lung
35	chr19:41773800-41787800	Strong transcription	Fetal Lung	lung
36	chr19:41773800-41788000	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr19:41773800-41788000	Strong transcription	Brain Angular Gyrus	brain
38	chr19:41773800-41788000	Strong transcription	Brain Hippocampus Middle	brain
39	chr19:41773800-41788600	Strong transcription	NHDF-Ad	bronchial
40	chr19:41773800-41790800	Strong transcription	HepG2	liver
41	chr19:41773800-41793800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr19:41773800-41794600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:41773800-41798400	Strong transcription	Adipose Nuclei	Adipose
44	chr19:41773800-41800200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr19:41773800-41800200	Strong transcription	Fetal Intestine Large	intestine
46	chr19:41773800-41800200	Strong transcription	Fetal Intestine Small	intestine
47	chr19:41773800-41801400	Strong transcription	HMEC	breast
48	chr19:41773800-41801600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:41773800-41801600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:41773800-41801600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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