Variant report

Variant	rs10171850
Chromosome Location	chr2:172006741-172006742
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	chr2:172002500..172008778-chr2:172012564..172018500,9	MCF-7	breast:
2	chr2:172004769..172008425-chr2:172014877..172017754,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198586	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10177560	0.96[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs10182205	0.85[EUR][1000 genomes]
rs10183486	0.92[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs10183909	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10186343	0.84[EUR][1000 genomes]
rs10191270	0.96[CEU][hapmap]
rs10198197	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10199500	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs10204062	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10208271	0.85[EUR][1000 genomes]
rs10208341	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10210693	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs10210791	0.84[EUR][1000 genomes]
rs10210883	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs1025240	0.88[CEU][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs1025241	0.84[EUR][1000 genomes]
rs1035825	0.92[CEU][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs1035827	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.87[ASN][1000 genomes]
rs1035828	0.97[TSI][hapmap]
rs10803855	0.83[EUR][1000 genomes]
rs10930453	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10930455	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10930456	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10930457	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs11674590	0.83[EUR][1000 genomes]
rs11696064	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12467411	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs12473741	0.95[CHB][hapmap];0.83[CHD][hapmap]
rs12477649	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12612871	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs12614580	0.82[EUR][1000 genomes]
rs12618232	0.85[ASN][1000 genomes]
rs12618898	0.87[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12624094	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13004273	0.92[CEU][hapmap];0.97[TSI][hapmap]
rs13008199	0.92[CEU][hapmap];0.97[TSI][hapmap]
rs13010307	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs13025198	0.84[EUR][1000 genomes]
rs13030784	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs13034529	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs13036123	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs13395669	0.83[EUR][1000 genomes]
rs13401706	0.85[EUR][1000 genomes]
rs13402107	0.84[EUR][1000 genomes]
rs13403285	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs13410683	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13411575	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs13419444	0.85[EUR][1000 genomes]
rs13425247	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs13427723	0.85[EUR][1000 genomes]
rs13428613	0.85[EUR][1000 genomes]
rs13430489	0.85[EUR][1000 genomes]
rs13432813	0.85[EUR][1000 genomes]
rs1344237	0.96[CEU][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs1529378	0.92[CEU][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs1529391	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs16859142	0.83[EUR][1000 genomes]
rs16859157	0.81[CHB][hapmap]
rs1863679	0.86[CHB][hapmap]
rs1978592	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs1989613	0.86[CHB][hapmap]
rs2033160	0.81[CEU][hapmap];0.97[TSI][hapmap]
rs2081715	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2114596	0.84[EUR][1000 genomes]
rs2195117	0.81[EUR][1000 genomes]
rs2217154	0.85[EUR][1000 genomes]
rs2356599	0.83[EUR][1000 genomes]
rs2356608	0.96[CEU][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs2557794	0.92[CEU][hapmap]
rs2676131	0.81[CEU][hapmap];0.97[TSI][hapmap]
rs2676151	0.92[CEU][hapmap];0.97[TSI][hapmap]
rs34518725	0.84[EUR][1000 genomes]
rs35173138	0.85[EUR][1000 genomes]
rs35312173	0.83[EUR][1000 genomes]
rs35988467	0.83[EUR][1000 genomes]
rs3731990	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3731993	0.81[CHB][hapmap]
rs3755121	0.92[CEU][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs3770419	0.86[CHB][hapmap]
rs3770423	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs3770428	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs3770433	0.92[CEU][hapmap]
rs4564745	0.96[CEU][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs4667673	0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs4668354	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4668355	0.88[CEU][hapmap]
rs4668368	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs5028603	0.80[CEU][hapmap]
rs55758155	0.85[EUR][1000 genomes]
rs55996750	0.80[EUR][1000 genomes]
rs56402728	0.85[EUR][1000 genomes]
rs56405950	0.84[EUR][1000 genomes]
rs6433276	0.92[CEU][hapmap];0.97[TSI][hapmap]
rs6433282	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6714164	0.88[CEU][hapmap];0.97[TSI][hapmap]
rs6716127	0.96[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs6722537	0.82[EUR][1000 genomes]
rs6730417	0.92[CEU][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs6732229	0.84[EUR][1000 genomes]
rs6733178	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs6734542	0.82[EUR][1000 genomes]
rs6742854	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6749427	0.81[EUR][1000 genomes]
rs6750849	0.82[EUR][1000 genomes]
rs6754315	0.90[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs6761596	0.84[EUR][1000 genomes]
rs6761642	0.92[CEU][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs728455	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7421377	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs754058	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]
rs7560360	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7578491	0.83[EUR][1000 genomes]
rs7580629	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs7581195	0.84[EUR][1000 genomes]
rs7581314	0.80[EUR][1000 genomes]
rs7582822	0.92[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7585418	0.81[EUR][1000 genomes]
rs7593193	0.81[CEU][hapmap]
rs7594071	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7603316	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs7603460	0.85[EUR][1000 genomes]
rs7606502	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs7606822	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs930035	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs930036	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs958183	0.83[EUR][1000 genomes]
rs964172	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10171850	TLK1	cis	normal skin	skin_eQTL
rs10171850	TLK1	cis	lesional skin	skin_eQTL
rs10171850	TLK1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171957200-172010400	Weak transcription	HSMM	muscle
2	chr2:171973600-172011000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:171988200-172014400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:171989400-172007000	Weak transcription	Lung	lung
5	chr2:171990000-172016000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:171994000-172010400	Weak transcription	Thymus	Thymus
7	chr2:171994200-172010400	Weak transcription	Ovary	ovary
8	chr2:171995400-172012200	Weak transcription	Dnd41	blood
9	chr2:171996600-172015400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:171996600-172015400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:171996600-172015600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:171997000-172007600	Weak transcription	Placenta	Placenta
13	chr2:171997000-172010400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:171998200-172007200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:171998200-172010400	Weak transcription	Psoas Muscle	Psoas
16	chr2:171998400-172014800	Weak transcription	Brain Anterior Caudate	brain
17	chr2:171999000-172014800	Weak transcription	Osteobl	bone
18	chr2:171999200-172014000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:171999600-172012200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:171999600-172013800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:172000000-172010400	Weak transcription	Spleen	Spleen
22	chr2:172000200-172014600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr2:172001000-172010800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:172001600-172010400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:172002000-172007600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:172003000-172012200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:172003200-172007600	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr2:172003200-172015400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr2:172003400-172008800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr2:172003400-172010400	Weak transcription	Fetal Thymus	thymus
31	chr2:172003400-172012200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:172003600-172008400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:172003600-172010800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:172003600-172014600	Weak transcription	HMEC	breast
35	chr2:172003800-172010400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:172003800-172012400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:172003800-172014600	Weak transcription	NH-A	brain
38	chr2:172004000-172006800	Weak transcription	A549	lung
39	chr2:172004000-172010400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:172004000-172012600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:172004200-172009800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:172004200-172010800	Weak transcription	NHEK	skin
43	chr2:172004200-172015400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:172004400-172007000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:172004800-172009400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr2:172004800-172010000	Weak transcription	Primary B cells from cord blood	blood
47	chr2:172004800-172010000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:172004800-172010400	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:172005000-172009800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr2:172005000-172010000	Weak transcription	K562	blood

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