Variant report

Variant	rs1111695
Chromosome Location	chr1:114243899-114243900
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114240356..114244592-chr1:114247076..114250656,5	K562	blood:
2	chr1:114242321..114244665-chr7:108476146..108478634,2	MCF-7	breast:
3	chr1:114240657..114244104-chr1:114245278..114249575,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116793	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10858016	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10858017	0.81[YRI][hapmap]
rs11102671	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12061482	0.89[ASW][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1217200	0.81[YRI][hapmap]
rs1217234	0.89[LWK][hapmap]
rs1217235	0.90[YRI][hapmap]
rs1217378	0.87[ASN][1000 genomes]
rs1217379	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs1217385	0.82[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap]
rs1217405	0.84[ASN][1000 genomes]
rs1217406	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs1217409	0.83[ASN][1000 genomes]
rs1217411	0.87[ASN][1000 genomes]
rs1217418	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs1217419	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs1217420	0.83[ASN][1000 genomes]
rs1230682	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1230685	0.81[YRI][hapmap]
rs1230686	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1235005	0.95[CHD][hapmap];0.97[GIH][hapmap]
rs1310182	0.87[ASN][1000 genomes]
rs1539437	0.89[ASN][1000 genomes]
rs1743605	0.89[LWK][hapmap]
rs1777241	0.89[ASW][hapmap];0.89[LWK][hapmap]
rs1936398	0.89[ASW][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1981319	0.89[ASW][hapmap];0.85[LWK][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes]
rs2146019	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2185971	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2273758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2295853	0.89[ASW][hapmap];0.85[LWK][hapmap]
rs2476600	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs2476604	0.81[ASN][1000 genomes]
rs2797412	0.81[YRI][hapmap]
rs2797414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2797416	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs3789598	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3789600	0.82[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs4423005	0.90[AFR][1000 genomes]
rs4600045	0.89[ASW][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4991898	0.85[ASN][1000 genomes]
rs6537795	0.87[AFR][1000 genomes]
rs6537798	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs6663679	0.90[AFR][1000 genomes]
rs6665194	0.90[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap]
rs6672018	0.82[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs6696784	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6698586	0.89[ASW][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7553188	0.90[AFR][1000 genomes]
rs7555634	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs7556622	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv872161	chr1:114162194-114280135	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1111695	PHTF1	cis	cerebellum	SCAN
rs1111695	SIKE1	cis	parietal	SCAN
rs1111695	PHTF1	cis	parietal	SCAN
rs1111695	PHTF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114203200-114298600	Weak transcription	Fetal Brain Male	brain
2	chr1:114216000-114247000	Weak transcription	HMEC	breast
3	chr1:114216200-114279800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:114216400-114250400	Weak transcription	Placenta	Placenta
5	chr1:114220400-114263800	Weak transcription	Fetal Kidney	kidney
6	chr1:114227000-114268200	Weak transcription	NHLF	lung
7	chr1:114227400-114252000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:114228000-114287800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:114228400-114249800	Weak transcription	Hela-S3	cervix
10	chr1:114231000-114251200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:114233200-114245000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:114236400-114300000	Weak transcription	Small Intestine	intestine
13	chr1:114237400-114256600	Weak transcription	Colonic Mucosa	Colon
14	chr1:114238000-114251400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:114238000-114252800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:114238000-114258200	Weak transcription	Fetal Heart	heart
17	chr1:114238200-114250200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:114238200-114252200	Weak transcription	Fetal Brain Female	brain
19	chr1:114238200-114256000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:114238200-114264400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:114238400-114244400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:114238400-114266800	Weak transcription	NHEK	skin
23	chr1:114238800-114251000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:114238800-114252400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr1:114238800-114252800	Weak transcription	Fetal Intestine Large	intestine
26	chr1:114238800-114252800	Weak transcription	K562	blood
27	chr1:114239000-114244200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:114239000-114260400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:114239200-114279800	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:114239400-114258600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:114239600-114244200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:114239600-114244400	Strong transcription	GM12878-XiMat	blood
33	chr1:114239600-114245400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:114239600-114249800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr1:114239800-114244200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:114239800-114244200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr1:114239800-114250800	Weak transcription	HepG2	liver
38	chr1:114240200-114244000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:114240200-114260800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:114240200-114279400	Weak transcription	Psoas Muscle	Psoas
41	chr1:114242000-114244200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr1:114242000-114244800	Weak transcription	Primary B cells from cord blood	blood
43	chr1:114242000-114247000	Weak transcription	NH-A	brain
44	chr1:114242000-114300000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:114242200-114244000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr1:114242200-114245000	Weak transcription	Osteobl	bone
47	chr1:114242200-114246600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:114242200-114246600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:114242200-114246800	Weak transcription	Adipose Nuclei	Adipose
50	chr1:114242200-114246800	Weak transcription	Liver	Liver

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