Variant report

Variant	rs8105161
Chromosome Location	chr19:41839631-41839632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41837922..41839964-chr19:41843309..41846016,2	K562	blood:
2	chr19:41838935..41840441-chr19:41859912..41861504,2	K562	blood:
3	chr19:41828482..41836150-chr19:41836490..41842395,12	K562	blood:

Variant related genes	Relation type
ENSG00000142046	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10410836	0.91[ASN][1000 genomes]
rs10421990	0.91[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.94[ASN][1000 genomes]
rs1056854	0.91[CEU][hapmap]
rs11466347	0.98[EUR][1000 genomes]
rs11466359	0.83[EUR][1000 genomes]
rs11879562	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]
rs11880564	0.83[EUR][1000 genomes]
rs11881940	0.91[CEU][hapmap]
rs12327659	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]
rs12972949	0.84[EUR][1000 genomes]
rs12974323	0.94[ASN][1000 genomes]
rs12974420	0.91[CEU][hapmap]
rs12975585	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs12975920	0.92[ASN][1000 genomes]
rs12978323	0.87[JPT][hapmap]
rs12980298	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12980480	0.80[ASW][hapmap];0.91[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12980839	0.89[ASN][1000 genomes]
rs12980942	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12981053	0.95[EUR][1000 genomes]
rs12983047	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12984160	1.00[CEU][hapmap]
rs12985162	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs12985339	0.91[CEU][hapmap]
rs13345456	0.94[ASN][1000 genomes]
rs16958994	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16958996	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16958999	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16959007	0.83[YRI][hapmap]
rs16975124	0.87[YRI][hapmap]
rs16975156	0.83[YRI][hapmap]
rs16975164	0.87[YRI][hapmap]
rs1865051	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]
rs1865052	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1865053	1.00[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2053086	0.91[CEU][hapmap]
rs2241718	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2241719	0.83[EUR][1000 genomes]
rs2241720	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2304230	0.80[ASW][hapmap];0.91[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.88[YRI][hapmap];0.91[ASN][1000 genomes]
rs2304234	0.87[JPT][hapmap]
rs34075897	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34945449	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3745295	0.86[ASW][hapmap];0.91[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.83[YRI][hapmap];0.91[ASN][1000 genomes]
rs3752705	0.80[ASW][hapmap];0.91[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3810173	0.82[YRI][hapmap]
rs3816052	0.91[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.91[ASN][1000 genomes]
rs3826714	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4456618	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802112	0.88[JPT][hapmap]
rs61459202	0.84[EUR][1000 genomes]
rs66724427	0.91[ASN][1000 genomes]
rs67511749	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6957	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7245398	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7248164	0.91[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.94[ASN][1000 genomes]
rs7254679	0.82[CEU][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7256416	0.91[ASN][1000 genomes]
rs7256856	0.91[ASN][1000 genomes]
rs7257310	0.93[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7257742	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7257825	0.90[ASN][1000 genomes]
rs7258749	0.91[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]
rs747857	0.83[YRI][hapmap]
rs8103839	0.91[CEU][hapmap]
rs8105901	0.91[CEU][hapmap]
rs8109167	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]
rs8109627	0.81[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs998468	0.83[YRI][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	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
rs8105161	TSKS	cis	parietal	SCAN
rs8105161	FLT3LG	cis	cerebellum	SCAN
rs8105161	BAX	cis	cerebellum	SCAN
rs8105161	PLEKHA4	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41818600-41854800	Strong transcription	Dnd41	blood
2	chr19:41832400-41856000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr19:41833400-41846400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:41834200-41839800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:41834200-41842000	Genic enhancers	Placenta	Placenta
6	chr19:41834200-41842600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr19:41834200-41856600	Weak transcription	Brain Anterior Caudate	brain
8	chr19:41834200-41856800	Weak transcription	Fetal Kidney	kidney
9	chr19:41834400-41854800	Weak transcription	Small Intestine	intestine
10	chr19:41834600-41842600	Strong transcription	Thymus	Thymus
11	chr19:41834800-41840000	Genic enhancers	Primary monocytes fromperipheralblood	blood
12	chr19:41834800-41841400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:41834800-41845200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr19:41834800-41845600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:41834800-41847600	Weak transcription	Brain Hippocampus Middle	brain
16	chr19:41834800-41849400	Weak transcription	Fetal Lung	lung
17	chr19:41834800-41855600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr19:41834800-41856800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr19:41834800-41856800	Weak transcription	Brain Substantia Nigra	brain
20	chr19:41835000-41840400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:41835000-41841600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
22	chr19:41835000-41843400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:41835000-41845200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr19:41835000-41845600	Weak transcription	HSMM	muscle
25	chr19:41835000-41847600	Weak transcription	Gastric	stomach
26	chr19:41835000-41847800	Weak transcription	Pancreas	Pancrea
27	chr19:41835000-41854400	Strong transcription	Fetal Stomach	stomach
28	chr19:41835000-41856600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr19:41835000-41856800	Weak transcription	Brain Angular Gyrus	brain
30	chr19:41835200-41843600	Weak transcription	NH-A	brain
31	chr19:41835200-41846600	Weak transcription	HMEC	breast
32	chr19:41835200-41849400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr19:41835400-41840000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
34	chr19:41835400-41841200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr19:41835400-41845800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:41835400-41847600	Weak transcription	Colonic Mucosa	Colon
37	chr19:41835400-41847800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr19:41835600-41856000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:41835800-41840400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:41836000-41855200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:41836200-41840000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr19:41836200-41845200	Strong transcription	Osteobl	bone
43	chr19:41836800-41839800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr19:41836800-41840600	Weak transcription	HSMMtube	muscle
45	chr19:41836800-41840600	Strong transcription	HUVEC	blood vessel
46	chr19:41836800-41841400	Strong transcription	Fetal Thymus	thymus
47	chr19:41836800-41843000	Strong transcription	Primary T cells from cord blood	blood
48	chr19:41837200-41840000	Strong transcription	Primary B cells from cord blood	blood
49	chr19:41837200-41847600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr19:41837200-41847600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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