Variant report

Variant	rs12788348
Chromosome Location	chr11:9790088-9790089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9780866..9785648-chr11:9787509..9790769,4	K562	blood:
2	chr11:9780268..9785648-chr11:9787366..9790238,5	K562	blood:

Variant related genes	Relation type
ENSG00000245522	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1032550	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10770060	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10770064	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10770065	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10840305	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840306	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042493	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1875029	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1875030	0.91[EUR][1000 genomes]
rs1983002	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1996794	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34328537	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34690050	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35401279	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360136	1.00[JPT][hapmap]
rs360137	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs360147	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360157	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs3751000	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs415895	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs429835	0.95[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs440377	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4910063	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4910499	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7126913	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7934930	0.85[ASN][1000 genomes]
rs7935673	0.86[ASN][1000 genomes]
rs960909	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers 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	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1045550	chr11:9718324-9790088	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12788348	SWAP70	cis	lymphoblastoid	seeQTL
rs12788348	ILK	cis	cerebellum	SCAN
rs12788348	SWAP70	cis	multi-tissue	Pritchard
rs12788348	OR52E6	cis	parietal	SCAN
rs12788348	SWAP70	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9780600-9813200	Weak transcription	Small Intestine	intestine
2	chr11:9780800-9794200	Enhancers	Fetal Muscle Leg	muscle
3	chr11:9781400-9795200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:9781400-9800800	Weak transcription	Fetal Brain Female	brain
5	chr11:9781600-9798200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr11:9781600-9801000	Weak transcription	Primary T cells from cord blood	blood
7	chr11:9781600-9809000	Weak transcription	Fetal Brain Male	brain
8	chr11:9781800-9790800	Enhancers	NHDF-Ad	bronchial
9	chr11:9781800-9799200	Weak transcription	Primary B cells from cord blood	blood
10	chr11:9781800-9799200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr11:9781800-9801200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr11:9781800-9801600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr11:9782000-9798000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:9782200-9796200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr11:9782400-9791600	Weak transcription	A549	lung
16	chr11:9782400-9799400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:9782600-9797800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr11:9784000-9797200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:9784000-9801200	Weak transcription	Gastric	stomach
20	chr11:9784400-9797000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr11:9787400-9790800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr11:9787400-9792600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr11:9787400-9796200	Weak transcription	Esophagus	oesophagus
24	chr11:9787400-9796200	Weak transcription	Psoas Muscle	Psoas
25	chr11:9787400-9796800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr11:9787400-9799000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:9787400-9801000	Weak transcription	Aorta	Aorta
28	chr11:9787600-9792400	Weak transcription	Fetal Intestine Small	intestine
29	chr11:9787600-9796000	Weak transcription	Hela-S3	cervix
30	chr11:9787600-9797600	Weak transcription	Fetal Intestine Large	intestine
31	chr11:9787600-9799200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr11:9787600-9799200	Weak transcription	Fetal Lung	lung
33	chr11:9787800-9795800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr11:9787800-9796200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr11:9787800-9801000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr11:9787800-9805200	Weak transcription	Colonic Mucosa	Colon
37	chr11:9788000-9791200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr11:9788000-9792600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:9788000-9796000	Weak transcription	Ovary	ovary
40	chr11:9788000-9796200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:9788000-9796200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:9788000-9796200	Weak transcription	Right Atrium	heart
43	chr11:9788000-9796600	Weak transcription	Pancreas	Pancrea
44	chr11:9788000-9801000	Weak transcription	Lung	lung
45	chr11:9788200-9795400	Weak transcription	Osteobl	bone
46	chr11:9788200-9796200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr11:9788200-9796200	Weak transcription	Right Ventricle	heart
48	chr11:9788200-9801000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:9788400-9790600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr11:9788400-9791400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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