Variant report

Variant	rs4668354
Chromosome Location	chr2:171814750-171814751
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:171789845..171791695-chr2:171813662..171815924,2	K562	blood:
2	chr2:171806216..171808590-chr2:171814117..171816828,2	MCF-7	breast:
3	chr2:171813561..171816045-chr2:171817049..171819064,3	K562	blood:
4	chr2:171787073..171789315-chr2:171814638..171817447,2	K562	blood:

Variant related genes	Relation type
ENSG00000115806	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10171850	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10177560	0.88[CEU][hapmap]
rs10183486	0.84[CEU][hapmap]
rs10191270	0.96[CEU][hapmap]
rs10198197	0.92[CEU][hapmap]
rs10199500	0.92[CEU][hapmap]
rs10208341	0.92[CEU][hapmap]
rs10210693	0.84[CEU][hapmap]
rs10210883	0.92[CEU][hapmap]
rs1025240	0.88[CEU][hapmap]
rs1035825	0.92[CEU][hapmap]
rs1035827	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10803853	0.87[EUR][1000 genomes]
rs10803854	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs10930448	0.91[EUR][1000 genomes]
rs10930449	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs10930453	0.92[CEU][hapmap]
rs10930455	0.92[CEU][hapmap]
rs10930456	0.92[CEU][hapmap]
rs10930457	0.92[CEU][hapmap]
rs11686985	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11696064	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11902360	0.84[ASN][1000 genomes]
rs11902369	0.89[CEU][hapmap];0.96[CHB][hapmap];0.96[JPT][hapmap];0.84[ASN][1000 genomes]
rs11904750	0.86[CHB][hapmap]
rs12467411	0.82[CHB][hapmap]
rs12471930	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12473741	0.86[CHB][hapmap]
rs12477649	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12612871	0.96[CEU][hapmap];0.93[YRI][hapmap];0.92[EUR][1000 genomes]
rs12618898	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs12621769	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13004273	0.92[CEU][hapmap]
rs13008199	0.92[CEU][hapmap]
rs13010307	0.92[CEU][hapmap]
rs13025033	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13030784	0.92[CEU][hapmap]
rs13034529	0.92[CEU][hapmap]
rs13036123	0.91[CEU][hapmap]
rs13403285	0.95[CEU][hapmap]
rs13410683	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs13411575	0.92[CEU][hapmap]
rs13425247	0.92[CEU][hapmap]
rs1344237	0.88[CEU][hapmap]
rs1529378	0.92[CEU][hapmap]
rs1529391	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs16859050	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16859157	0.83[CHB][hapmap]
rs17505447	0.83[CHB][hapmap]
rs1978592	0.92[CEU][hapmap]
rs2033160	0.81[CEU][hapmap]
rs2059723	0.86[CHB][hapmap]
rs2081715	0.92[CEU][hapmap]
rs2081767	0.86[CHB][hapmap]
rs2081768	0.87[CHB][hapmap]
rs2098999	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2114738	0.88[EUR][1000 genomes]
rs2195116	0.88[CEU][hapmap]
rs2356422	0.87[CHB][hapmap]
rs2356423	0.86[ASN][1000 genomes]
rs2356608	0.88[CEU][hapmap]
rs2555922	0.84[CEU][hapmap]
rs2557794	0.92[CEU][hapmap]
rs2676131	0.81[CEU][hapmap]
rs2676151	0.92[CEU][hapmap]
rs2723241	0.81[CEU][hapmap]
rs3731993	0.83[CHB][hapmap]
rs3755121	0.92[CEU][hapmap]
rs3755124	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3755126	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3770423	0.92[CEU][hapmap]
rs3770428	0.92[CEU][hapmap]
rs3770433	0.92[CEU][hapmap]
rs3770436	0.81[CHB][hapmap]
rs3770438	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]
rs4564745	0.88[CEU][hapmap]
rs4667667	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4667673	0.92[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];0.87[YRI][hapmap];0.88[ASN][1000 genomes]
rs4668343	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4668344	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4668345	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4668346	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4668349	0.92[EUR][1000 genomes]
rs4668350	0.90[EUR][1000 genomes]
rs4668355	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs4668368	0.81[CEU][hapmap]
rs5028603	0.81[CEU][hapmap]
rs6433266	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6433267	0.89[EUR][1000 genomes]
rs6433276	0.92[CEU][hapmap]
rs6714164	0.88[CEU][hapmap]
rs6714300	0.92[EUR][1000 genomes]
rs6716127	0.88[CEU][hapmap]
rs6729847	0.88[EUR][1000 genomes]
rs6730417	0.92[CEU][hapmap]
rs6731774	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6733178	0.92[CEU][hapmap]
rs6742564	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6742797	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs6754315	0.91[CEU][hapmap]
rs6760293	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6761642	0.92[CEU][hapmap]
rs731693	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7421377	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs754058	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs7559136	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7560889	0.83[ASN][1000 genomes]
rs7567927	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7570701	0.91[EUR][1000 genomes]
rs7580629	0.81[CEU][hapmap]
rs7585607	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7593193	0.82[CEU][hapmap]
rs7598194	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7603316	0.88[CEU][hapmap]
rs7606822	0.91[CEU][hapmap]
rs930035	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs930036	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs964172	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs965518	0.87[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4668354	TLK1	cis	lesional skin	skin_eQTL
rs4668354	TLK1	Cis_1M	lymphoblastoid	RTeQTL
rs4668354	TLK1	cis	uninvolved skin	skin_eQTL
rs4668354	TLK1	cis	normal skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171787600-171829800	Weak transcription	Right Atrium	heart
2	chr2:171797000-171830600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:171803600-171824600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:171803800-171824400	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:171803800-171825600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr2:171804000-171825000	Strong transcription	HepG2	liver
7	chr2:171804600-171817400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:171804800-171824800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:171804800-171825800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:171805000-171817400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:171805000-171819600	Strong transcription	K562	blood
12	chr2:171805000-171824800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:171805000-171825000	Strong transcription	Dnd41	blood
14	chr2:171805200-171824800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:171805400-171814800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:171805400-171816400	Strong transcription	NHEK	skin
17	chr2:171805400-171824600	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:171805400-171825000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:171805400-171825200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:171805400-171825400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:171805400-171825600	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr2:171805400-171825800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:171805400-171825800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:171805600-171815200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:171805600-171816600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:171805600-171817400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:171805600-171821800	Strong transcription	HSMM	muscle
28	chr2:171805600-171824600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:171805600-171824600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:171805600-171825800	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr2:171805800-171818400	Strong transcription	Adipose Nuclei	Adipose
32	chr2:171805800-171821800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:171805800-171823800	Strong transcription	NHDF-Ad	bronchial
34	chr2:171805800-171825200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr2:171805800-171825800	Strong transcription	Placenta	Placenta
36	chr2:171805800-171825800	Strong transcription	Osteobl	bone
37	chr2:171805800-171826200	Strong transcription	Fetal Thymus	thymus
38	chr2:171806000-171814800	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr2:171806000-171814800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:171806000-171814800	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:171806000-171815000	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr2:171806000-171815000	Strong transcription	Colonic Mucosa	Colon
43	chr2:171806000-171816000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:171806000-171816000	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr2:171806000-171816200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:171806000-171821200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:171806000-171821600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:171806000-171821600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:171806000-171821800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:171806000-171821800	Strong transcription	NH-A	brain

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