Variant report

Variant	rs1944108
Chromosome Location	chr11:93464175-93464176
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:93459602-93466128	GM12891	blood:	n/a	n/a
2	POLR2A	chr11:93460818-93464251	GM12892	blood:	n/a	n/a
3	POLR2A	chr11:93460755-93469030	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr11:93458130-93475423	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr11:93460047-93464370	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr11:93460289-93472162	K562	blood:	n/a	n/a
7	POLR2A	chr11:93460849-93475367	GM18505	blood:	n/a	n/a
8	POLR2A	chr11:93460250-93475527	HepG2	liver:	n/a	n/a
9	POLR2A	chr11:93459876-93475383	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr11:93460999-93464241	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr11:93463599-93464302	K562	blood:	n/a	n/a
12	POLR2A	chr11:93460923-93464848	K562	blood:	n/a	n/a
13	POLR2A	chr11:93460023-93475421	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:93460130-93464309	HepG2	liver:	n/a	n/a
15	POLR2A	chr11:93459739-93464343	MCF-7	breast:	n/a	n/a
16	POLR2A	chr11:93464113-93464349	HepG2	liver:	n/a	n/a
17	POLR2A	chr11:93460630-93475546	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr11:93459725-93466147	GM12878	blood:	n/a	n/a
19	POLR2A	chr11:93459823-93475456	HepG2	liver:	n/a	n/a
20	POLR2A	chr11:93460391-93464286	GM19099	blood:	n/a	n/a
21	POLR2A	chr11:93460087-93466232	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr11:93460512-93464298	GM12892	blood:	n/a	n/a
23	POLR2A	chr11:93463597-93464449	HL-60	blood:	n/a	n/a
24	POLR2A	chr11:93459661-93475348	K562	blood:	n/a	n/a
25	MBD4	chr11:93463687-93464192	HepG2	liver:	n/a	n/a
26	POLR2A	chr11:93463479-93464192	GM12878	blood:	n/a	n/a
27	POLR2A	chr11:93460693-93469181	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr11:93464138-93464334	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr11:93460303-93464426	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr11:93460248-93464478	NB4	blood:	n/a	n/a
31	POLR2A	chr11:93460792-93464591	HCT-116	colon:	n/a	n/a
32	POLR2A	chr11:93460770-93475249	K562	blood:	n/a	n/a
33	POLR2A	chr11:93460670-93468979	A549	lung:	n/a	n/a
34	POLR2A	chr11:93460475-93464886	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr11:93460801-93464255	GM12892	blood:	n/a	n/a
36	POLR2A	chr11:93459992-93464913	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr11:93460780-93464322	K562	blood:	n/a	n/a
38	POLR2A	chr11:93459344-93464275	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr11:93459539-93465301	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr11:93460803-93464338	GM12892	blood:	n/a	n/a
41	POLR2A	chr11:93463548-93464222	K562	blood:	n/a	n/a
42	POLR2A	chr11:93460837-93464291	HepG2	liver:	n/a	n/a
43	POLR2A	chr11:93460982-93466115	K562	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:93459100..93466497-chr11:93514555..93520746,14	K562	blood:
2	chr11:93462890..93477443-chr11:93512595..93526939,73	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VSTM5-1	chr11:93463833-93464382	NONHSAT023669
2	lnc-VSTM5-1	chr11:93463843-93464382	NONHSAT023663

No data

Variant related genes	Relation type
SNORA25	TF binding region
ENSG00000166012	Chromatin interaction
ENSG00000042429	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10741469	0.89[EUR][1000 genomes]
rs10765619	0.88[EUR][1000 genomes]
rs10765623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1080367	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10831082	0.91[EUR][1000 genomes]
rs10831083	0.92[EUR][1000 genomes]
rs10831084	0.80[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes]
rs11020478	0.84[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11020479	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11529070	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1939568	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2186685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4363551	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4376865	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4619111	0.88[EUR][1000 genomes]
rs4753485	0.90[EUR][1000 genomes]
rs603360	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs694699	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7111796	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7925086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9888134	0.88[EUR][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	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv898182	chr11:93381845-93637462	Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv832232	chr11:93401314-93549438	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1944108	C11orf54	cis	cerebellum	SCAN
rs1944108	SCARNA9	cis	cerebellum	SCAN
rs1944108	MED17	cis	cerebellum	SCAN
rs1944108	SCARNA9	cis	parietal	SCAN
rs1944108	MED17	cis	parietal	SCAN
rs1944108	C11orf54	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93427000-93465800	Strong transcription	Hela-S3	cervix
2	chr11:93430800-93465400	Weak transcription	Stomach Mucosa	stomach
3	chr11:93444000-93466400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:93444800-93471000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:93445400-93465200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:93447600-93468000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:93448000-93465600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:93448600-93465400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr11:93449200-93471800	Weak transcription	Right Atrium	heart
10	chr11:93449400-93465400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:93449600-93471800	Weak transcription	Esophagus	oesophagus
12	chr11:93450600-93471800	Weak transcription	Gastric	stomach
13	chr11:93450600-93473000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:93451600-93469800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:93451600-93470800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:93451800-93466800	Strong transcription	Dnd41	blood
17	chr11:93453200-93468000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr11:93453400-93465200	Strong transcription	Duodenum Mucosa	Duodenum
19	chr11:93453600-93468000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr11:93453800-93465200	Strong transcription	Fetal Intestine Large	intestine
21	chr11:93453800-93471200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr11:93453800-93471800	Strong transcription	Fetal Muscle Leg	muscle
23	chr11:93453800-93471800	Strong transcription	Fetal Thymus	thymus
24	chr11:93453800-93472400	Strong transcription	Fetal Muscle Trunk	muscle
25	chr11:93454000-93470400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr11:93454200-93467000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr11:93454400-93467800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:93454400-93469000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr11:93454400-93469400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr11:93454400-93469600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr11:93454400-93469800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:93454400-93470000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr11:93454400-93470800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr11:93454400-93471000	Strong transcription	Fetal Lung	lung
35	chr11:93454600-93471000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr11:93454600-93471000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr11:93454800-93471000	Strong transcription	Adipose Nuclei	Adipose
38	chr11:93455000-93466000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr11:93455000-93468000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr11:93455000-93471200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr11:93455000-93471800	Strong transcription	Placenta	Placenta
42	chr11:93455200-93467800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:93457400-93465800	Strong transcription	Fetal Brain Female	brain
44	chr11:93457400-93470200	Strong transcription	Brain Cingulate Gyrus	brain
45	chr11:93457600-93467800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr11:93458200-93464600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr11:93458200-93465200	Strong transcription	Liver	Liver
48	chr11:93458400-93465400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr11:93458400-93467800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:93458400-93471800	Strong transcription	Stomach Smooth Muscle	stomach

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