Variant report

Variant	rs11858844
Chromosome Location	chr15:77792260-77792261
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77711973..77714541-chr15:77791132..77792971,2	K562	blood:
2	chr15:77789312..77792548-chr15:77795862..77798378,3	K562	blood:

Variant related genes	Relation type
ENSG00000173517	Chromatin interaction
ENSG00000140382	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11853696	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11856084	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12324211	0.89[ASN][1000 genomes]
rs12324795	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12912084	0.82[ASN][1000 genomes]
rs13380202	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16968897	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs16968900	0.83[EUR][1000 genomes]
rs17384809	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17385059	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17385296	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17385352	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17470529	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17470952	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17471252	0.82[ASN][1000 genomes]
rs17471431	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17471480	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17471697	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17471753	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17472200	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2012740	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2012756	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2307141	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28437977	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2864840	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3784787	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3784788	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886863	0.82[ASN][1000 genomes]
rs4886864	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886865	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56097641	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59204923	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs59362734	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59386622	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61306472	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62007297	0.83[ASN][1000 genomes]
rs74026910	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74026912	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74026913	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74026918	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74026923	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74026925	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs74026926	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8035526	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs907398	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
4	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS 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	11 gene(s)	inside rSNPs	diseases
6	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv570140	chr15:77787469-77851535	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11858844	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77777600-77798600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:77785600-77792400	Enhancers	Fetal Muscle Leg	muscle
3	chr15:77786200-77793400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr15:77786200-77794000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr15:77786200-77800000	Weak transcription	Thymus	Thymus
6	chr15:77786400-77799600	Weak transcription	Primary B cells from cord blood	blood
7	chr15:77786400-77803800	Weak transcription	Primary T cells from cord blood	blood
8	chr15:77787600-77792400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:77789800-77792400	Enhancers	Fetal Muscle Trunk	muscle
10	chr15:77789800-77796400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:77789800-77798600	Weak transcription	Gastric	stomach
12	chr15:77789800-77799600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:77789800-77801000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:77790000-77792600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr15:77790000-77793200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:77790000-77793200	Weak transcription	NHEK	skin
17	chr15:77790200-77793200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:77790200-77799200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr15:77790600-77793200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:77790600-77799200	Weak transcription	GM12878-XiMat	blood
21	chr15:77790800-77793600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr15:77791000-77793200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:77791000-77794200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:77791000-77794800	Weak transcription	HepG2	liver
25	chr15:77791000-77796000	Weak transcription	Liver	Liver
26	chr15:77791000-77797000	Weak transcription	Lung	lung
27	chr15:77791000-77797400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:77791000-77797400	Weak transcription	Pancreas	Pancrea
29	chr15:77791000-77797800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr15:77791000-77798600	Weak transcription	HSMM	muscle
31	chr15:77791000-77798800	Weak transcription	Fetal Intestine Large	intestine
32	chr15:77791200-77793200	Weak transcription	HMEC	breast
33	chr15:77791200-77795600	Weak transcription	Placenta	Placenta
34	chr15:77791200-77796200	Weak transcription	Esophagus	oesophagus
35	chr15:77791200-77796800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:77791200-77797000	Weak transcription	Fetal Intestine Small	intestine
37	chr15:77791400-77793400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:77791600-77793400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:77791600-77793400	Weak transcription	Right Ventricle	heart
40	chr15:77791600-77794600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:77791600-77795400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr15:77791600-77795600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:77791600-77796000	Weak transcription	Spleen	Spleen
44	chr15:77791600-77797000	Weak transcription	Fetal Brain Female	brain
45	chr15:77791600-77798600	Weak transcription	Fetal Kidney	kidney
46	chr15:77791600-77798800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:77791600-77798800	Weak transcription	Osteobl	bone
48	chr15:77791600-77799000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr15:77791800-77793600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:77791800-77795400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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