Variant report

Variant	rs3793941
Chromosome Location	chr11:71721407-71721408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:71719288-71721535	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr11:71720922-71721407	GM12891	blood:	n/a	n/a
3	POLR2A	chr11:71711262-71721775	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:71710254-71727597	Hela-S3	cervix:	n/a	n/a
5	MTA3	chr11:71721177-71722085	GM12878	blood:	n/a	n/a
6	BCL3	chr11:71721119-71723592	A549	lung:	n/a	chr11:71721976-71721985 chr11:71722842-71722851 chr11:71721935-71721944
7	POLR2A	chr11:71720783-71722029	HepG2	liver:	n/a	n/a
8	POLR2A	chr11:71720420-71723286	K562	blood:	n/a	n/a
9	POLR2A	chr11:71710901-71724979	A549	lung:	n/a	n/a
10	POLR2A	chr11:71720450-71721621	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr11:71720336-71723646	Hela-S3	cervix:	n/a	n/a
12	NFATC1	chr11:71720978-71721589	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:71721040-71722875	GM19193	blood:	n/a	n/a
14	POLR2A	chr11:71720843-71721520	U87	brain:	n/a	n/a
15	POLR2A	chr11:71721353-71721851	HepG2	liver:	n/a	n/a
16	POLR2A	chr11:71721398-71721600	GM12891	blood:	n/a	n/a
17	POLR2A	chr11:71721045-71721770	GM12878	blood:	n/a	n/a
18	POLR2A	chr11:71720578-71721573	HepG2	liver:	n/a	n/a
19	POLR2A	chr11:71717636-71723316	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr11:71720921-71722618	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr11:71707765-71727247	K562	blood:	n/a	n/a
22	POLR2A	chr11:71720234-71722694	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr11:71720374-71722961	HepG2	liver:	n/a	n/a
24	NFATC1	chr11:71720387-71721546	GM12878	blood:	n/a	n/a
25	POLR2A	chr11:71720328-71722855	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr11:71711657-71723922	GM12891	blood:	n/a	n/a
27	POLR2A	chr11:71720841-71721785	GM12892	blood:	n/a	n/a
28	POLR2A	chr11:71719835-71723045	GM12878	blood:	n/a	n/a
29	POLR2A	chr11:71720868-71722148	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr11:71720878-71723118	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr11:71720781-71721538	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr11:71720490-71721526	PANC-1	pancreas:	n/a	n/a
33	POLR2A	chr11:71720247-71721421	GM12891	blood:	n/a	n/a
34	POLR2A	chr11:71720279-71723602	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:71718667..71720612-chr11:71720770..71724717,3	MCF-7	breast:
2	chr11:71704932..71706691-chr11:71720292..71722192,2	K562	blood:
3	chr11:71721358..71722982-chr11:71723674..71725357,2	K562	blood:
4	chr11:71709478..71712665-chr11:71718866..71721839,3	K562	blood:
5	chr11:71716531..71721205-chr11:71721229..71725488,7	K562	blood:

No data

Variant related genes	Relation type
NUMA1	TF binding region
ENSG00000251143	TF binding region
ENSG00000137522	Chromatin interaction
ENSG00000137496	Chromatin interaction
ENSG00000251143	Chromatin interaction
ENSG00000137497	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10898815	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10898820	0.96[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs4073394	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs7939902	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv428262	chr11:71363639-71804055	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers 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	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3793941	IL18BP	cis	cerebellum	SCAN
rs3793941	P2RY2	cis	parietal	SCAN
rs3793941	FAM86C1	cis	Adipose Subcutaneous	GTEx
rs3793941	FAM86C1	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71677200-71736600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:71705400-71734400	Strong transcription	Fetal Intestine Small	intestine
3	chr11:71709400-71723800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:71709600-71722400	Strong transcription	Fetal Brain Female	brain
5	chr11:71709600-71737000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:71709800-71735800	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr11:71709800-71736600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr11:71709800-71748000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:71710200-71735600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:71710600-71735800	Strong transcription	Brain Germinal Matrix	brain
11	chr11:71710600-71736000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:71710800-71734200	Strong transcription	Fetal Intestine Large	intestine
13	chr11:71710800-71734800	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr11:71710800-71735600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:71710800-71735800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:71710800-71743200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr11:71710800-71748000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:71711000-71723800	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr11:71711000-71735800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:71711000-71736600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr11:71711000-71741800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:71711000-71748800	Strong transcription	Dnd41	blood
23	chr11:71711200-71722200	Weak transcription	Right Atrium	heart
24	chr11:71711200-71742400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr11:71711400-71723400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr11:71711400-71723400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr11:71711400-71723800	Strong transcription	Liver	Liver
28	chr11:71711400-71725200	Strong transcription	Thymus	Thymus
29	chr11:71711400-71735800	Strong transcription	Osteobl	bone
30	chr11:71711400-71736400	Strong transcription	GM12878-XiMat	blood
31	chr11:71711400-71747600	Strong transcription	Fetal Thymus	thymus
32	chr11:71711600-71721600	Strong transcription	Brain Angular Gyrus	brain
33	chr11:71711600-71723800	Strong transcription	Adipose Nuclei	Adipose
34	chr11:71711600-71723800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr11:71711600-71724000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr11:71711600-71724200	Strong transcription	Colonic Mucosa	Colon
37	chr11:71711600-71735200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr11:71711600-71735600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr11:71711600-71735800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr11:71711600-71736400	Strong transcription	Primary T cells from cord blood	blood
41	chr11:71711600-71736600	Strong transcription	Fetal Lung	lung
42	chr11:71711600-71747800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr11:71711800-71723200	Strong transcription	Gastric	stomach
44	chr11:71711800-71723200	Strong transcription	NHLF	lung
45	chr11:71711800-71735800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:71711800-71736400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr11:71711800-71736400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr11:71711800-71736400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr11:71711800-71736600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr11:71711800-71737800	Strong transcription	Sigmoid Colon	Sigmoid Colon

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