Variant report

Variant	rs2359167
Chromosome Location	chr1:114299516-114299517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114299428..114302166-chr1:114446012..114448303,2	K562	blood:
2	chr1:114298167..114305255-chr1:114351008..114356451,27	MCF-7	breast:
3	chr1:114299507..114303267-chr1:114354438..114356409,4	K562	blood:
4	chr1:114299235..114302663-chr1:114470274..114473459,3	K562	blood:
5	chr1:114299035..114300595-chr1:114352639..114355622,2	K562	blood:
6	chr1:114289765..114292253-chr1:114298221..114300505,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231128	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000163349	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10858005	0.81[CHB][hapmap]
rs10858007	0.81[CHB][hapmap];0.81[TSI][hapmap]
rs10858008	0.81[CHB][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs10858011	0.81[CHB][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap]
rs10858017	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10858018	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10858019	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10858021	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11102654	0.81[CHB][hapmap]
rs11102669	0.81[EUR][1000 genomes]
rs11102691	0.86[JPT][hapmap]
rs1113523	0.86[CHB][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs1146182	0.82[CEU][hapmap];0.85[CHB][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs1146187	0.82[CEU][hapmap];0.86[CHB][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs12041547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12044534	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12061482	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12063216	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1217192	0.81[CEU][hapmap];0.81[CHB][hapmap];0.86[TSI][hapmap]
rs1217193	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs1217199	0.81[CHB][hapmap]
rs1217200	0.82[CEU][hapmap];0.86[CHB][hapmap];0.84[TSI][hapmap]
rs1217201	0.81[CHB][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs1217210	0.82[EUR][1000 genomes]
rs1217211	0.86[CHB][hapmap]
rs1217226	0.81[CHB][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs1217227	0.81[CHB][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs1217228	0.81[CHB][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs1217234	0.81[CHB][hapmap];0.84[TSI][hapmap]
rs1217235	0.81[CHB][hapmap]
rs1217236	0.80[TSI][hapmap]
rs1217376	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1217377	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1217380	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1217386	0.85[ASN][1000 genomes]
rs1217388	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1217389	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1217395	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1217396	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1217407	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1217410	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1217412	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1217413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217415	0.86[CHB][hapmap];0.87[TSI][hapmap]
rs1217416	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217421	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1230637	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1230638	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1230639	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1230640	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1230642	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1230645	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1230646	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1230647	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1230649	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1230655	0.82[EUR][1000 genomes]
rs1230656	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1230658	0.82[CEU][hapmap];0.86[CHB][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1230659	0.82[CEU][hapmap];0.86[CHB][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1230661	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1230671	0.82[EUR][1000 genomes]
rs1230678	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1230679	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1230683	0.82[EUR][1000 genomes]
rs1230685	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1230687	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1237289	0.81[CHB][hapmap]
rs1237682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12565589	0.82[CEU][hapmap];0.81[CHB][hapmap];0.84[TSI][hapmap]
rs12566340	0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs1343125	0.82[GIH][hapmap];0.81[TSI][hapmap]
rs1343128	0.81[CHB][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap]
rs1418958	0.81[CHB][hapmap]
rs1599971	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17031716	0.86[CHB][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs1743605	0.82[CEU][hapmap];0.86[CHB][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs1746853	0.81[CHB][hapmap]
rs1775754	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1777234	0.81[CEU][hapmap]
rs1777237	0.82[CEU][hapmap];0.86[CHB][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs1777238	0.82[EUR][1000 genomes]
rs1777241	0.82[CEU][hapmap];0.81[CHB][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1935838	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1936398	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1981319	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2093436	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2243471	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2295853	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2358816	0.94[CEU][hapmap]
rs2358994	1.00[ASW][hapmap]
rs2488457	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2488458	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2636013	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2636014	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2797408	0.89[EUR][1000 genomes]
rs2797409	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2797412	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2798135	0.81[EUR][1000 genomes]
rs2798138	0.81[EUR][1000 genomes]
rs3761936	1.00[ASW][hapmap]
rs4145859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4423005	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4565712	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4600045	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4838997	0.82[EUR][1000 genomes]
rs4839335	0.84[EUR][1000 genomes]
rs61817589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6537792	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs6537795	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6663679	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6689879	0.81[CHB][hapmap]
rs6698586	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6704188	0.81[CHB][hapmap]
rs7526209	0.88[ASN][1000 genomes]
rs7529353	0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs7553188	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9429730	0.80[CEU][hapmap];0.86[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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2359167	PHTF1	cis	cerebellum	SCAN
rs2359167	SIKE1	cis	parietal	SCAN
rs2359167	MAGI3	cis	parietal	SCAN
rs2359167	PHTF1	cis	parietal	SCAN
rs2359167	MAGI3	cis	cerebellum	SCAN
rs2359167	CD58	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114236400-114300000	Weak transcription	Small Intestine	intestine
2	chr1:114242000-114300000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:114245600-114300600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:114258000-114300000	Weak transcription	Right Ventricle	heart
5	chr1:114261400-114300000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:114261400-114300600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:114261400-114301000	Weak transcription	Lung	lung
8	chr1:114261600-114300200	Weak transcription	Brain Angular Gyrus	brain
9	chr1:114261600-114300600	Weak transcription	Aorta	Aorta
10	chr1:114261600-114300600	Weak transcription	Esophagus	oesophagus
11	chr1:114261600-114300600	Weak transcription	Gastric	stomach
12	chr1:114263600-114300000	Weak transcription	Fetal Lung	lung
13	chr1:114263600-114300400	Weak transcription	Fetal Intestine Large	intestine
14	chr1:114264000-114300400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:114264200-114300000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:114267400-114300000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:114272800-114300000	Weak transcription	Primary B cells from cord blood	blood
18	chr1:114279800-114300200	Weak transcription	Fetal Kidney	kidney
19	chr1:114280400-114300000	Weak transcription	Psoas Muscle	Psoas
20	chr1:114280400-114301400	Weak transcription	Spleen	Spleen
21	chr1:114280600-114300200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:114280600-114300200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:114280800-114300000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:114281200-114300000	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:114281200-114300000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:114287200-114300200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:114287200-114300200	Weak transcription	Brain Substantia Nigra	brain
28	chr1:114288200-114300000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:114288400-114300000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:114288800-114300200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:114288800-114300200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:114289000-114300000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:114289800-114299800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:114290600-114300400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:114290800-114300000	Weak transcription	HMEC	breast
36	chr1:114290800-114300200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:114291400-114300000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:114292400-114300000	Weak transcription	Adipose Nuclei	Adipose
39	chr1:114292600-114300200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:114292800-114299800	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr1:114293000-114300000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr1:114293200-114300600	Weak transcription	Placenta	Placenta
43	chr1:114293400-114299800	Weak transcription	Fetal Stomach	stomach
44	chr1:114293400-114300600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:114294400-114299800	Weak transcription	NH-A	brain
46	chr1:114294600-114300000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:114295000-114300000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr1:114297000-114299800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:114297000-114299800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr1:114297000-114299800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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