Variant report

Variant	rs11102691
Chromosome Location	chr1:114421313-114421314
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114418599..114421976-chr1:114424069..114426568,3	MCF-7	breast:
2	chr1:114419011..114421363-chr1:114446430..114449267,2	K562	blood:
3	chr1:114415525..114417374-chr1:114419070..114421891,2	K562	blood:
4	chr1:114420803..114423426-chr1:114446345..114447908,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BCL2L15-1	chr1:114420790-114424619	NONHSAT005342

Variant related genes	Relation type
ENSG00000134262	Chromatin interaction
ENSG00000118655	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10858017	0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs10858018	0.95[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs10858019	0.86[EUR][1000 genomes]
rs10858021	0.86[EUR][1000 genomes]
rs11102689	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12041547	0.86[JPT][hapmap]
rs12044534	0.86[EUR][1000 genomes]
rs12060836	1.00[YRI][hapmap]
rs12061482	0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs12063216	0.86[EUR][1000 genomes]
rs12069381	1.00[YRI][hapmap]
rs12071676	1.00[YRI][hapmap]
rs12094790	1.00[YRI][hapmap]
rs1217376	0.86[EUR][1000 genomes]
rs1217377	0.95[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs1217380	0.95[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs1217386	0.82[EUR][1000 genomes]
rs1217388	0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.90[EUR][1000 genomes]
rs1217389	0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1217395	0.95[CEU][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1217396	0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes]
rs1217407	0.95[CEU][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1217410	0.95[CEU][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1217412	0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.89[EUR][1000 genomes]
rs1217413	0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs1217415	0.91[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap]
rs1217416	0.81[EUR][1000 genomes]
rs1217421	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1230638	0.85[EUR][1000 genomes]
rs1230639	0.85[EUR][1000 genomes]
rs1230640	0.82[ASW][hapmap];0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs1230645	0.82[ASW][hapmap];0.95[CEU][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs1230647	0.82[ASW][hapmap];0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1230649	0.82[ASW][hapmap];0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs1230658	0.80[EUR][1000 genomes]
rs1230659	0.80[EUR][1000 genomes]
rs1230678	0.86[EUR][1000 genomes]
rs1230679	0.86[EUR][1000 genomes]
rs1230685	0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs1230687	0.85[EUR][1000 genomes]
rs1237682	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs12566340	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1599971	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1775754	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1935838	0.83[EUR][1000 genomes]
rs1936398	0.95[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs1981319	0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs2093436	0.86[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs2243471	0.81[EUR][1000 genomes]
rs2295853	0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2358816	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2358994	0.83[MEX][hapmap]
rs2359167	0.86[JPT][hapmap]
rs2488457	0.82[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2488458	0.95[CEU][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2636013	0.95[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2636014	0.84[EUR][1000 genomes]
rs2797408	0.86[EUR][1000 genomes]
rs2797409	0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs2797412	0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs4145859	0.86[JPT][hapmap]
rs4423005	0.84[EUR][1000 genomes]
rs4565712	0.86[EUR][1000 genomes]
rs4600045	0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs4838997	0.80[EUR][1000 genomes]
rs4839335	0.81[EUR][1000 genomes]
rs6537792	0.80[EUR][1000 genomes]
rs6537795	0.86[EUR][1000 genomes]
rs6663679	0.84[EUR][1000 genomes]
rs6698586	0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs7529353	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7553188	0.84[EUR][1000 genomes]
rs9429730	0.95[CEU][hapmap];0.85[YRI][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11102691	MAGI3	cis	parietal	SCAN
rs11102691	PHTF1	cis	cerebellum	SCAN
rs11102691	CAPZA1	cis	parietal	SCAN
rs11102691	MAGI3	cis	cerebellum	SCAN
rs11102691	PHTF1	cis	parietal	SCAN

Chromatin state (count:40 , 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	chr1:114417600-114421800	Weak transcription	Primary T cells from cord blood	blood
9	chr1:114417600-114422000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:114417600-114423600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:114417600-114428800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:114417800-114421400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:114417800-114421600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:114417800-114421800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr1:114417800-114423200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr1:114418200-114421600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:114418600-114421600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:114418800-114421600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:114418800-114422000	Weak transcription	Small Intestine	intestine
20	chr1:114419000-114421600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:114419000-114421800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:114419000-114422000	Weak transcription	Fetal Intestine Large	intestine
23	chr1:114419000-114422000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:114419000-114427800	Weak transcription	Pancreas	Pancrea
25	chr1:114419800-114421800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:114420200-114437800	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:114420200-114446400	Weak transcription	Aorta	Aorta
28	chr1:114420600-114421600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:114421000-114423400	Enhancers	Primary T cells fromperipheralblood	blood
30	chr1:114421000-114423600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:114421000-114423600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:114421000-114424200	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr1:114421000-114424600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:114421000-114424600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr1:114421000-114424800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:114421200-114421600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:114421200-114421600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr1:114421200-114421600	Weak transcription	Fetal Intestine Small	intestine
39	chr1:114421200-114422600	Enhancers	GM12878-XiMat	blood
40	chr1:114421200-114424400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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