Variant report

Variant	rs11236410
Chromosome Location	chr11:75080920-75080921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:75061282..75063321-chr11:75080294..75083043,2	K562	blood:
2	chr11:75056296..75059058-chr11:75079339..75081796,2	MCF-7	breast:
3	chr11:75073760..75076326-chr11:75079019..75081067,2	K562	blood:

Variant related genes	Relation type
ENSG00000137486	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10899087	0.91[EUR][1000 genomes]
rs11236404	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236406	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236409	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236411	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236414	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11827957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11828411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12270709	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12274798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12278382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12278562	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12280035	0.87[YRI][hapmap]
rs12293208	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12797588	0.85[CEU][hapmap]
rs34786358	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35281674	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4509790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123202	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7929742	0.91[EUR][1000 genomes]
rs7931083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041640	chr11:74945824-75174688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
2	nsv832211	chr11:74945839-75106125	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
3	nsv516556	chr11:75071783-75080920	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11236410	LIPT2	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75064200-75086800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:75077200-75083000	Weak transcription	Fetal Lung	lung
3	chr11:75077600-75083200	Weak transcription	Adipose Nuclei	Adipose
4	chr11:75077800-75081600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr11:75078200-75082800	Weak transcription	K562	blood
6	chr11:75079200-75083000	Weak transcription	Placenta	Placenta
7	chr11:75080000-75081200	ZNF genes & repeats	Dnd41	blood
8	chr11:75080200-75081400	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr11:75080400-75081200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr11:75080400-75081400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr11:75080400-75081400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:75080600-75081200	Enhancers	Primary B cells from cord blood	blood
13	chr11:75080600-75081200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr11:75080600-75081200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr11:75080600-75081200	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr11:75080600-75081400	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr11:75080600-75081400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:75080600-75081600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr11:75080600-75083600	Enhancers	Primary hematopoietic stem cells	blood
20	chr11:75080800-75081000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:75080800-75081000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr11:75080800-75081000	Enhancers	Colonic Mucosa	Colon
23	chr11:75080800-75081000	Enhancers	Duodenum Mucosa	Duodenum
24	chr11:75080800-75081000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr11:75080800-75081000	Enhancers	Lung	lung
26	chr11:75080800-75081000	Bivalent Enhancer	GM12878-XiMat	blood
27	chr11:75080800-75081200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr11:75080800-75081200	Enhancers	Primary B cells from peripheral blood	blood
29	chr11:75080800-75081200	Enhancers	Primary T cells from cord blood	blood
30	chr11:75080800-75081200	Enhancers	Primary T cells fromperipheralblood	blood
31	chr11:75080800-75081200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr11:75080800-75081200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr11:75080800-75081200	Enhancers	Gastric	stomach
34	chr11:75080800-75081200	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr11:75080800-75081200	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr11:75080800-75081200	Enhancers	Spleen	Spleen
37	chr11:75080800-75081200	Enhancers	Hela-S3	cervix
38	chr11:75080800-75081400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr11:75080800-75081400	Enhancers	HUVEC	blood vessel
40	chr11:75080800-75081800	Enhancers	Stomach Mucosa	stomach

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