Variant report

Variant	rs12618898
Chromosome Location	chr2:171890306-171890307
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:171889760..171896240-chr2:171897516..171901220,6	K562	blood:
2	chr2:171889636..171891864-chr2:172289797..172291819,2	MCF-7	breast:
3	chr2:171886698..171888644-chr2:171888783..171890639,2	K562	blood:

Variant related genes	Relation type
ENSG00000123600	Chromatin interaction
ENSG00000115827	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10171850	0.87[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs10177560	0.83[CEU][hapmap]
rs10191270	0.92[CEU][hapmap]
rs10198197	0.88[CEU][hapmap]
rs10199500	0.88[CEU][hapmap]
rs10208341	0.88[CEU][hapmap]
rs10210883	0.92[CEU][hapmap]
rs1025240	0.84[CEU][hapmap]
rs1035825	0.87[CEU][hapmap]
rs1035827	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10803854	0.92[CEU][hapmap]
rs10930449	0.92[CEU][hapmap]
rs10930453	0.88[CEU][hapmap]
rs10930455	0.88[CEU][hapmap]
rs10930456	0.88[CEU][hapmap]
rs10930457	0.88[CEU][hapmap]
rs11696064	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11902369	0.84[CEU][hapmap];0.86[CHB][hapmap];0.96[JPT][hapmap]
rs12467411	0.80[CHB][hapmap]
rs12473741	0.84[CHB][hapmap]
rs12477649	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12612871	0.92[CEU][hapmap];0.90[YRI][hapmap]
rs12618232	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12624094	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13004273	0.87[CEU][hapmap]
rs13008199	0.87[CEU][hapmap]
rs13010307	0.88[CEU][hapmap]
rs13030784	0.88[CEU][hapmap]
rs13034529	0.88[CEU][hapmap]
rs13036123	0.86[CEU][hapmap]
rs13403285	0.94[CEU][hapmap]
rs13410683	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13411575	0.88[CEU][hapmap]
rs13425247	0.88[CEU][hapmap]
rs1344237	0.83[CEU][hapmap]
rs1529378	0.87[CEU][hapmap]
rs1529391	0.87[CEU][hapmap]
rs16859050	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs16859157	0.81[CHB][hapmap]
rs1978592	0.87[CEU][hapmap]
rs2081715	0.88[CEU][hapmap]
rs2098999	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2195116	0.83[CEU][hapmap]
rs2195117	0.80[EUR][1000 genomes]
rs2356608	0.83[CEU][hapmap]
rs2555922	0.80[CEU][hapmap]
rs2557794	0.87[CEU][hapmap]
rs2676151	0.87[CEU][hapmap]
rs2723241	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs3731990	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3731993	0.81[CHB][hapmap]
rs3755121	0.87[CEU][hapmap]
rs3755124	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3755126	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3770423	0.88[CEU][hapmap]
rs3770428	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs3770433	0.88[CEU][hapmap]
rs3770438	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap]
rs4564745	0.83[CEU][hapmap]
rs4667673	0.88[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4668343	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4668354	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs4668355	0.92[CEU][hapmap]
rs6433276	0.87[CEU][hapmap]
rs6714164	0.83[CEU][hapmap]
rs6716127	0.83[CEU][hapmap]
rs6719647	0.86[EUR][1000 genomes]
rs6730417	0.87[CEU][hapmap]
rs6733178	0.88[CEU][hapmap]
rs6742564	0.81[ASN][1000 genomes]
rs6742797	0.92[CEU][hapmap]
rs6742854	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6754315	0.86[CEU][hapmap]
rs6761642	0.87[CEU][hapmap]
rs731693	0.92[CEU][hapmap]
rs7421377	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs754058	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]
rs7582822	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs7603316	0.84[CEU][hapmap]
rs7606822	0.91[CEU][hapmap]
rs930035	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs930036	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs964172	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12618898	TLK1	cis	uninvolved skin	skin_eQTL
rs12618898	TLK1	cis	lesional skin	skin_eQTL
rs12618898	TLK1	cis	normal skin	skin_eQTL
rs12618898	TLK1	Cis_1M	lymphoblastoid	RTeQTL

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	chr2:171830800-171891400	Weak transcription	Spleen	Spleen
3	chr2:171831400-171916200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:171841000-171895800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:171841600-171940000	Weak transcription	Right Ventricle	heart
6	chr2:171842200-171892000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:171842600-171912000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:171846000-171898000	Weak transcription	Psoas Muscle	Psoas
9	chr2:171846200-171901000	Weak transcription	Fetal Brain Male	brain
10	chr2:171847400-171902600	Weak transcription	Brain Angular Gyrus	brain
11	chr2:171850400-171892000	Weak transcription	Brain Anterior Caudate	brain
12	chr2:171853200-171898800	Weak transcription	Aorta	Aorta
13	chr2:171858000-171891800	Weak transcription	Fetal Brain Female	brain
14	chr2:171858000-171892000	Weak transcription	Brain Substantia Nigra	brain
15	chr2:171859400-171892000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:171859600-171897000	Weak transcription	Esophagus	oesophagus
17	chr2:171862200-171890600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr2:171862600-171918400	Weak transcription	Brain Germinal Matrix	brain
19	chr2:171862800-171899000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:171862800-171931200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:171863200-171896200	Weak transcription	Hela-S3	cervix
22	chr2:171865800-171905000	Weak transcription	Fetal Heart	heart
23	chr2:171867800-171898600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:171867800-171898800	Weak transcription	Colonic Mucosa	Colon
25	chr2:171867800-171916200	Weak transcription	Gastric	stomach
26	chr2:171868000-171890800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:171868200-171891800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:171871200-171897800	Weak transcription	Pancreas	Pancrea
29	chr2:171871400-171891200	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:171871400-171898000	Weak transcription	Lung	lung
31	chr2:171871600-171892000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:171873000-171891600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:171874800-171916200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:171875000-171892200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr2:171877400-171890400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr2:171877800-171892200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:171878000-171891800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:171878000-171943200	Weak transcription	Small Intestine	intestine
39	chr2:171878200-171892200	Weak transcription	HUVEC	blood vessel
40	chr2:171878600-171891800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:171878800-171893600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr2:171878800-171940000	Weak transcription	Stomach Mucosa	stomach
43	chr2:171879000-171892400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:171879200-171891000	Weak transcription	A549	lung
45	chr2:171879800-171891600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:171879800-171891800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:171879800-171891800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:171879800-171892000	Weak transcription	Left Ventricle	heart
49	chr2:171879800-171892000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:171879800-171892000	Weak transcription	Thymus	Thymus

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