Variant report

Variant	rs6665194
Chromosome Location	chr1:114417843-114417844
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114416696..114418511-chr1:114445493..114447564,2	K562	blood:
2	chr1:114416299..114419266-chr1:114473123..114475526,3	MCF-7	breast:
3	chr1:114416727..114419302-chr20:56273752..56275590,2	MCF-7	breast:
4	chr1:114410354..114414312-chr1:114415133..114418521,4	K562	blood:
5	chr1:114414556..114418668-chr1:114471915..114474547,3	K562	blood:
6	chr1:114391365..114395021-chr1:114417111..114420542,3	MCF-7	breast:
7	chr1:114351776..114354778-chr1:114417690..114420488,3	MCF-7	breast:
8	chr1:114377679..114378960-chr1:114416919..114417937,6	MCF-7	breast:
9	chr1:114415510..114417903-chr1:114447530..114449794,2	MCF-7	breast:
10	chr1:114417201..114419873-chr1:114437424..114440357,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000118655	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000134242	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000134262	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1111695	0.90[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap]
rs1217378	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1217379	0.82[CEU][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1217385	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217404	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1217405	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1217406	0.82[CEU][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1217409	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1217411	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1217414	0.81[LWK][hapmap]
rs1217418	0.81[CEU][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1217419	0.82[CEU][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1217420	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1230682	0.80[ASN][1000 genomes]
rs1230686	0.80[ASN][1000 genomes]
rs1235005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1310182	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1539437	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2185971	0.90[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap]
rs2273758	0.95[CHD][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap]
rs2476600	0.81[CEU][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2476604	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2797414	0.95[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs2797416	0.82[CEU][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3789598	0.95[CHD][hapmap];0.95[GIH][hapmap];0.83[LWK][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs3789600	0.82[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4991898	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6537798	0.82[CEU][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6672018	0.82[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs7555634	0.82[CEU][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats 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	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6665194	PTPN22	cis	cerebellum	SCAN
rs6665194	MAGI3	cis	parietal	SCAN
rs6665194	MAGI3	cis	cerebellum	SCAN
rs6665194	PHTF1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114415000-114447000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:114415200-114418200	Enhancers	Primary hematopoietic stem cells	blood
3	chr1:114415200-114418600	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr1:114415400-114419000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:114415400-114428800	Weak transcription	Colonic Mucosa	Colon
6	chr1:114415400-114437000	Weak transcription	Thymus	Thymus
7	chr1:114415600-114418000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr1:114415600-114418200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr1:114415600-114418400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr1:114415600-114418800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr1:114415800-114418200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:114415800-114418800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr1:114417000-114423600	Weak transcription	Stomach Mucosa	stomach
14	chr1:114417200-114419000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr1:114417200-114419200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:114417200-114437000	Weak transcription	Primary B cells from cord blood	blood
17	chr1:114417400-114418800	Enhancers	Small Intestine	intestine
18	chr1:114417400-114419000	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr1:114417400-114419200	Enhancers	Duodenum Mucosa	Duodenum
20	chr1:114417400-114421400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:114417400-114421800	Weak transcription	Dnd41	blood
22	chr1:114417600-114418000	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr1:114417600-114419000	Enhancers	GM12878-XiMat	blood
24	chr1:114417600-114419200	Enhancers	Fetal Intestine Small	intestine
25	chr1:114417600-114421000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr1:114417600-114421000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:114417600-114421800	Weak transcription	Primary T cells from cord blood	blood
28	chr1:114417600-114422000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:114417600-114423600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr1:114417600-114428800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:114417800-114419000	Enhancers	Fetal Intestine Large	intestine
32	chr1:114417800-114421000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:114417800-114421400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:114417800-114421600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:114417800-114421800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr1:114417800-114423200	Weak transcription	Monocytes-CD14+_RO01746	blood

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