Variant report

Variant	rs17108054
Chromosome Location	chr11:108343320-108343321
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:108343240-108343578	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000221607	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10890845	0.83[CHD][hapmap]
rs11825355	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs12278954	0.83[CHD][hapmap]
rs17107969	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[YRI][hapmap]
rs17107980	1.00[CHB][hapmap];0.84[YRI][hapmap]
rs17108024	0.83[CHD][hapmap]
rs17108065	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs2840346	1.00[GIH][hapmap]
rs28690878	1.00[GIH][hapmap]
rs3092836	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[YRI][hapmap]
rs3092856	1.00[CHB][hapmap]
rs4988050	1.00[CHB][hapmap]
rs4988131	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs7119791	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7131306	0.83[CHD][hapmap]
rs7931985	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[YRI][hapmap]

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	nsv1052254	chr11:108122683-108845008	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv541164	chr11:108122683-108845008	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv832263	chr11:108183372-108384391	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17108054	MGC33948	cis	multi-tissue	Pritchard
rs17108054	C11orf65	cis	multi-tissue	Pritchard
rs17108054	C11orf65	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108338200-108345400	Weak transcription	Gastric	stomach
2	chr11:108338200-108345600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:108338200-108345600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:108338200-108346200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:108338200-108359000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:108338200-108367600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:108338400-108347600	Weak transcription	Lung	lung
8	chr11:108338400-108352600	Weak transcription	Spleen	Spleen
9	chr11:108338600-108344400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:108338600-108347800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr11:108338600-108364800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr11:108338600-108367200	Weak transcription	A549	lung
13	chr11:108338600-108367800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr11:108338800-108343400	Weak transcription	NH-A	brain
15	chr11:108338800-108344000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr11:108338800-108344200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr11:108338800-108344200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:108338800-108344200	Weak transcription	HSMM	muscle
19	chr11:108338800-108344600	Weak transcription	Fetal Intestine Large	intestine
20	chr11:108338800-108345000	Weak transcription	Primary T cells from cord blood	blood
21	chr11:108338800-108345400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr11:108338800-108345400	Weak transcription	Aorta	Aorta
23	chr11:108338800-108345400	Weak transcription	Esophagus	oesophagus
24	chr11:108338800-108345400	Weak transcription	Fetal Stomach	stomach
25	chr11:108338800-108345400	Weak transcription	Ovary	ovary
26	chr11:108338800-108345400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr11:108338800-108345400	Weak transcription	Thymus	Thymus
28	chr11:108338800-108345600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:108338800-108345600	Weak transcription	Pancreas	Pancrea
30	chr11:108338800-108345800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr11:108338800-108347200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr11:108338800-108347400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr11:108338800-108347400	Weak transcription	Fetal Kidney	kidney
34	chr11:108338800-108347400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr11:108338800-108347600	Weak transcription	Colon Smooth Muscle	Colon
36	chr11:108338800-108347600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr11:108338800-108347800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr11:108338800-108347800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr11:108338800-108347800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:108338800-108347800	Weak transcription	Colonic Mucosa	Colon
41	chr11:108338800-108347800	Weak transcription	Left Ventricle	heart
42	chr11:108338800-108347800	Weak transcription	Right Ventricle	heart
43	chr11:108338800-108348200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr11:108338800-108349000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr11:108338800-108352400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr11:108338800-108354800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr11:108338800-108356800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr11:108338800-108356800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr11:108338800-108356800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr11:108338800-108357200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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