Variant report

Variant	rs754058
Chromosome Location	chr2:171893117-171893118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:171892758..171894367-chr2:172016065..172018177,2	MCF-7	breast:
2	chr2:171830458..171832703-chr2:171892970..171895411,2	K562	blood:
3	chr2:171889760..171896240-chr2:171897516..171901220,6	K562	blood:

Variant related genes	Relation type
ENSG00000198586	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10171850	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.80[ASN][1000 genomes]
rs10177560	0.90[TSI][hapmap]
rs10183486	0.87[TSI][hapmap]
rs1025240	0.90[TSI][hapmap]
rs1035825	0.90[TSI][hapmap]
rs1035827	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1035828	0.80[CEU][hapmap];0.90[TSI][hapmap]
rs10803854	0.81[CEU][hapmap]
rs10930449	0.81[CEU][hapmap]
rs11696064	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11902369	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12467411	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs12473741	0.95[CHB][hapmap];0.83[CHD][hapmap]
rs12477649	0.80[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.87[ASN][1000 genomes]
rs12612871	0.82[ASW][hapmap];0.81[CEU][hapmap];0.93[YRI][hapmap]
rs12618232	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12618898	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12624094	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13004273	0.90[TSI][hapmap]
rs13008199	0.90[TSI][hapmap]
rs13403285	0.89[CEU][hapmap]
rs13410683	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1344237	0.90[TSI][hapmap]
rs1529378	0.90[TSI][hapmap]
rs16859050	0.82[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap]
rs16859157	0.81[CHB][hapmap]
rs1863679	0.86[CHB][hapmap]
rs1978592	0.87[TSI][hapmap]
rs1989613	0.86[CHB][hapmap]
rs2033160	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs2098999	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2356608	0.90[TSI][hapmap]
rs2555922	0.91[CEU][hapmap]
rs2676131	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs2676151	0.90[TSI][hapmap]
rs2723241	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs3731990	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3731993	0.81[CHB][hapmap]
rs3755121	0.90[TSI][hapmap]
rs3755124	0.82[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs3755126	0.82[ASW][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs3770419	0.86[CHB][hapmap]
rs3770438	0.90[ASW][hapmap];0.80[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.80[TSI][hapmap];0.93[YRI][hapmap]
rs4564745	0.90[TSI][hapmap]
rs4667673	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs4668343	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4668354	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs4668355	0.81[CEU][hapmap]
rs4668368	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs5028603	0.88[CEU][hapmap]
rs6433276	0.90[TSI][hapmap]
rs6714164	0.90[TSI][hapmap]
rs6716127	0.85[TSI][hapmap]
rs6719647	0.94[EUR][1000 genomes]
rs6730417	0.90[TSI][hapmap]
rs6742564	0.80[ASN][1000 genomes]
rs6742797	0.81[CEU][hapmap]
rs6742854	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6761642	0.90[TSI][hapmap]
rs731693	0.81[CEU][hapmap]
rs7421377	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7580629	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs7582822	1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap]
rs7593193	0.88[CEU][hapmap]
rs7606822	0.82[CEU][hapmap]
rs930035	0.80[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.88[ASN][1000 genomes]
rs930036	0.80[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.89[ASN][1000 genomes]
rs964172	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431801	chr2:171721493-171966493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv834456	chr2:171874210-172014659	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs754058	TLK1	cis	normal skin	skin_eQTL
rs754058	GORASP2	cis	cerebellum	SCAN
rs754058	TLK1	cis	uninvolved skin	skin_eQTL
rs754058	TLK1	Cis_1M	lymphoblastoid	RTeQTL
rs754058	DLX1	cis	cerebellum	SCAN
rs754058	TLK1	cis	lesional skin	skin_eQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171830600-171902800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:171831400-171916200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:171841000-171895800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:171841600-171940000	Weak transcription	Right Ventricle	heart
5	chr2:171842600-171912000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:171846000-171898000	Weak transcription	Psoas Muscle	Psoas
7	chr2:171846200-171901000	Weak transcription	Fetal Brain Male	brain
8	chr2:171847400-171902600	Weak transcription	Brain Angular Gyrus	brain
9	chr2:171853200-171898800	Weak transcription	Aorta	Aorta
10	chr2:171859600-171897000	Weak transcription	Esophagus	oesophagus
11	chr2:171862600-171918400	Weak transcription	Brain Germinal Matrix	brain
12	chr2:171862800-171899000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:171862800-171931200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:171863200-171896200	Weak transcription	Hela-S3	cervix
15	chr2:171865800-171905000	Weak transcription	Fetal Heart	heart
16	chr2:171867800-171898600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:171867800-171898800	Weak transcription	Colonic Mucosa	Colon
18	chr2:171867800-171916200	Weak transcription	Gastric	stomach
19	chr2:171871200-171897800	Weak transcription	Pancreas	Pancrea
20	chr2:171871400-171898000	Weak transcription	Lung	lung
21	chr2:171874800-171916200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:171878000-171943200	Weak transcription	Small Intestine	intestine
23	chr2:171878800-171893600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:171878800-171940000	Weak transcription	Stomach Mucosa	stomach
25	chr2:171879800-171894200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:171881800-171899000	Strong transcription	Dnd41	blood
27	chr2:171882400-171900800	Weak transcription	NH-A	brain
28	chr2:171882600-171902200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:171883200-171893200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:171883200-171897200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:171883600-171895200	Strong transcription	Fetal Thymus	thymus
32	chr2:171883600-171916200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:171884200-171913000	Strong transcription	Liver	Liver
34	chr2:171885600-171902800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:171886000-171902200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr2:171886200-171893600	Strong transcription	K562	blood
37	chr2:171887400-171903200	Strong transcription	Primary hematopoietic stem cells	blood
38	chr2:171888200-171893400	Strong transcription	HSMM	muscle
39	chr2:171888200-171913800	Strong transcription	HepG2	liver
40	chr2:171888400-171893400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:171888400-171893400	Strong transcription	Adipose Nuclei	Adipose
42	chr2:171889000-171897800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr2:171890400-171893400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:171890400-171893800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:171890400-171893800	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr2:171890400-171901400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:171890400-171912800	Strong transcription	Placenta	Placenta
48	chr2:171890400-171917600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:171890600-171893200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:171890600-171893400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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