Variant report

Variant	rs1217384
Chromosome Location	chr1:114419760-114419761
allele	C/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	chr1:114418599..114421976-chr1:114424069..114426568,3	MCF-7	breast:
2	chr1:114409351..114410929-chr1:114418836..114421208,2	K562	blood:
3	chr1:114410951..114412541-chr1:114418200..114420420,2	MCF-7	breast:
4	chr1:114419011..114421363-chr1:114446430..114449267,2	K562	blood:
5	chr1:114415525..114417374-chr1:114419070..114421891,2	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	chr1:114417906..114420931-chr1:114435786..114438695,3	MCF-7	breast:
9	chr1:114417201..114419873-chr1:114437424..114440357,2	MCF-7	breast:
10	chr1:114418607..114420693-chr1:114436996..114439745,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134262	Chromatin interaction
ENSG00000118655	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10127930	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10489936	0.81[EUR][1000 genomes]
rs1080307	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1217394	1.00[ASW][hapmap]
rs12729708	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12730735	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12734625	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12735104	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12746609	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12748727	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12752932	0.84[EUR][1000 genomes]
rs12753351	0.82[EUR][1000 genomes]
rs12758546	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12760457	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13374352	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1539438	1.00[ASW][hapmap]
rs17274550	0.82[EUR][1000 genomes]
rs17274620	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17274634	0.82[EUR][1000 genomes]
rs17359302	0.82[EUR][1000 genomes]
rs17462614	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17509390	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1885454	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2040040	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2359173	0.82[EUR][1000 genomes]
rs2359174	0.82[EUR][1000 genomes]
rs2476601	1.00[LWK][hapmap]
rs34042871	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34341173	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34649199	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34698891	0.81[EUR][1000 genomes]
rs34857922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34877889	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35320278	0.82[EUR][1000 genomes]
rs35383900	0.82[EUR][1000 genomes]
rs35836713	0.82[EUR][1000 genomes]
rs36115604	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3747998	0.82[EUR][1000 genomes]
rs3748003	0.82[EUR][1000 genomes]
rs3752953	0.91[CEU][hapmap]
rs3761931	0.81[EUR][1000 genomes]
rs3789595	0.82[EUR][1000 genomes]
rs3789599	0.94[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap]
rs3789607	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3789609	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61817579	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs61817586	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61817617	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61820162	0.82[EUR][1000 genomes]
rs6668829	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6674848	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6703387	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7533391	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7533605	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7549685	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7555354	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1217384	CD58	cis	cerebellum	SCAN

Chromatin state (count:37 , 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	chr1:114415400-114428800	Weak transcription	Colonic Mucosa	Colon
3	chr1:114415400-114437000	Weak transcription	Thymus	Thymus
4	chr1:114417000-114423600	Weak transcription	Stomach Mucosa	stomach
5	chr1:114417200-114437000	Weak transcription	Primary B cells from cord blood	blood
6	chr1:114417400-114421400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:114417400-114421800	Weak transcription	Dnd41	blood
8	chr1:114417600-114421000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr1:114417600-114421000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:114417600-114421800	Weak transcription	Primary T cells from cord blood	blood
11	chr1:114417600-114422000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:114417600-114423600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:114417600-114428800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:114417800-114421000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:114417800-114421400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:114417800-114421600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:114417800-114421800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr1:114417800-114423200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:114418200-114421000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:114418200-114421000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:114418200-114421600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:114418600-114421200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:114418600-114421600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:114418800-114421000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:114418800-114421000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:114418800-114421600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:114418800-114422000	Weak transcription	Small Intestine	intestine
28	chr1:114419000-114421000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:114419000-114421200	Weak transcription	GM12878-XiMat	blood
30	chr1:114419000-114421600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:114419000-114421800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:114419000-114422000	Weak transcription	Fetal Intestine Large	intestine
33	chr1:114419000-114422000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:114419000-114427800	Weak transcription	Pancreas	Pancrea
35	chr1:114419200-114421000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:114419600-114419800	Enhancers	Duodenum Mucosa	Duodenum
37	chr1:114419600-114419800	Enhancers	Fetal Intestine Small	intestine

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