Variant report

Variant	rs3770438
Chromosome Location	chr2:171805785-171805786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:171804516..171806493-chr2:171828529..171830920,2	K562	blood:
2	chr2:171707564..171709152-chr2:171803981..171806562,2	K562	blood:

Variant related genes	Relation type
ENSG00000128683	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10183486	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs10191270	0.91[CEU][hapmap]
rs10198197	0.88[CEU][hapmap]
rs10208341	0.88[CEU][hapmap]
rs10210883	0.87[CEU][hapmap]
rs1025240	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs1035825	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs1035827	0.81[CEU][hapmap];0.81[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs1035828	0.85[TSI][hapmap]
rs10803853	0.89[EUR][1000 genomes]
rs10803854	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs10930448	0.94[EUR][1000 genomes]
rs10930449	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs10930453	0.88[CEU][hapmap]
rs10930455	0.88[CEU][hapmap]
rs10930456	0.88[CEU][hapmap]
rs10930457	0.88[CEU][hapmap]
rs11686985	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11696064	0.81[CHB][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs11902369	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12471930	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12473741	0.81[CHB][hapmap]
rs12477649	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap]
rs12612871	0.92[CEU][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs12618898	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap]
rs12621769	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13004273	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs13008199	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs13010307	0.88[CEU][hapmap]
rs13025033	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13030784	0.88[CEU][hapmap]
rs13034529	0.88[CEU][hapmap]
rs13036123	0.90[CEU][hapmap]
rs13403285	0.89[CEU][hapmap]
rs13410683	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs13411575	0.88[CEU][hapmap]
rs13425247	0.88[CEU][hapmap]
rs1344237	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs1529378	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs1529391	0.88[CEU][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs16859050	0.91[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1978592	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs2033160	0.85[TSI][hapmap]
rs2081715	0.88[CEU][hapmap]
rs2098999	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2114738	0.85[EUR][1000 genomes]
rs2195116	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs2356423	0.81[ASN][1000 genomes]
rs2356608	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs2557794	0.88[CEU][hapmap]
rs2676131	0.85[TSI][hapmap]
rs2676151	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs3755121	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs3755124	0.91[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3755126	0.91[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3770423	0.88[CEU][hapmap]
rs3770428	0.88[CEU][hapmap]
rs3770433	0.88[CEU][hapmap]
rs4564745	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs4667667	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4667673	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.82[ASN][1000 genomes]
rs4668343	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4668344	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4668345	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4668346	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4668349	0.94[EUR][1000 genomes]
rs4668350	0.91[EUR][1000 genomes]
rs4668354	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4668355	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs4668368	0.82[TSI][hapmap]
rs6433266	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6433267	0.90[EUR][1000 genomes]
rs6433276	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs6714164	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs6714300	0.94[EUR][1000 genomes]
rs6716127	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs6729847	0.90[EUR][1000 genomes]
rs6730417	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs6731774	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6733178	0.87[CEU][hapmap]
rs6742564	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6742797	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs6754315	0.86[CEU][hapmap]
rs6760293	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6761642	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs731693	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs7421377	0.88[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs754058	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]
rs7559136	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7567927	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7570701	0.94[EUR][1000 genomes]
rs7585607	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7598194	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7603316	0.84[CEU][hapmap]
rs7606822	0.86[CEU][hapmap]
rs930035	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs930036	0.92[CEU][hapmap];0.81[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap]
rs964172	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs965518	0.85[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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3770438	TLK1	cis	uninvolved skin	skin_eQTL
rs3770438	TLK1	cis	lesional skin	skin_eQTL
rs3770438	TLK1	Cis_1M	lymphoblastoid	RTeQTL
rs3770438	SP5	cis	cerebellum	SCAN
rs3770438	TLK1	cis	normal skin	skin_eQTL
rs3770438	GORASP2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171787000-171810400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:171787400-171806000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:171787400-171806000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:171787400-171806000	Weak transcription	Esophagus	oesophagus
5	chr2:171787400-171806000	Weak transcription	Psoas Muscle	Psoas
6	chr2:171787400-171807200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:171787400-171808200	Weak transcription	Aorta	Aorta
8	chr2:171787400-171810000	Weak transcription	Small Intestine	intestine
9	chr2:171787600-171806800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:171787600-171807600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:171787600-171829800	Weak transcription	Right Atrium	heart
12	chr2:171787800-171806000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:171787800-171806000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:171787800-171806200	Weak transcription	Fetal Kidney	kidney
15	chr2:171787800-171806600	Weak transcription	Fetal Brain Female	brain
16	chr2:171787800-171807000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:171787800-171807400	Weak transcription	Brain Germinal Matrix	brain
18	chr2:171787800-171809200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:171788000-171805800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr2:171788000-171806000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr2:171788000-171806000	Weak transcription	Brain Substantia Nigra	brain
22	chr2:171788000-171806200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:171788000-171806600	Weak transcription	Fetal Lung	lung
24	chr2:171788000-171806800	Weak transcription	Brain Anterior Caudate	brain
25	chr2:171788000-171806800	Weak transcription	A549	lung
26	chr2:171788000-171807600	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:171788000-171808400	Weak transcription	Brain Angular Gyrus	brain
28	chr2:171788200-171806200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:171788400-171806200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:171789400-171805800	Weak transcription	Osteobl	bone
31	chr2:171789400-171806000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:171789600-171810000	Weak transcription	Stomach Mucosa	stomach
33	chr2:171790600-171806000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr2:171791600-171806000	Weak transcription	Lung	lung
35	chr2:171792400-171806000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:171793400-171806000	Weak transcription	Thymus	Thymus
37	chr2:171793400-171806000	Weak transcription	NH-A	brain
38	chr2:171794000-171806000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:171794200-171805800	Weak transcription	Placenta	Placenta
40	chr2:171794200-171806000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:171794200-171806000	Weak transcription	Fetal Intestine Small	intestine
42	chr2:171794200-171806000	Weak transcription	Fetal Stomach	stomach
43	chr2:171794200-171806000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:171794200-171809200	Weak transcription	Pancreas	Pancrea
45	chr2:171794400-171805800	Weak transcription	Fetal Thymus	thymus
46	chr2:171794400-171806000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:171794400-171806000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:171794400-171806000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr2:171794400-171806000	Weak transcription	Gastric	stomach
50	chr2:171794400-171807200	Weak transcription	Spleen	Spleen

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