Variant report

Variant	rs12417272
Chromosome Location	chr11:64980426-64980427
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64979709-64980455	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:64979210-64980565	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr11:64979568-64980440	GM12892	blood:	n/a	n/a
4	POLR2A	chr11:64979996-64980483	HCT-116	colon:	n/a	n/a
5	POLR2A	chr11:64979307-64981815	K562	blood:	n/a	n/a
6	POLR2A	chr11:64979599-64980607	K562	blood:	n/a	n/a
7	POLR2A	chr11:64979934-64980429	HL-60	blood:	n/a	n/a
8	POLR2A	chr11:64979831-64980426	HepG2	liver:	n/a	n/a
9	POLR2A	chr11:64979995-64980463	U87	brain:	n/a	n/a
10	POLR2A	chr11:64979701-64980492	HCT-116	colon:	n/a	n/a
11	POLR2A	chr11:64980001-64980463	U87	brain:	n/a	n/a
12	POLR2A	chr11:64979366-64980524	GM12892	blood:	n/a	n/a
13	POLR2A	chr11:64979565-64982093	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr11:64979960-64980432	MCF-7	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64972801..64975129-chr11:64978366..64981061,2	MCF-7	breast:
2	chr11:64896573..64898665-chr11:64978684..64981304,2	K562	blood:
3	chr11:64935815..64939073-chr11:64978282..64980684,3	K562	blood:
4	chr11:64936901..64940048-chr11:64977014..64981623,6	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPDYC-1	chr11:64979974-64981116	l_492_chr11:64979303-64980906_76bGuttman_hLF

No data

Variant related genes	Relation type
SLC22A20	TF binding region
ENSG00000204710	Chromatin interaction
ENSG00000162298	Chromatin interaction
ENSG00000014216	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11605576	0.88[ASN][1000 genomes]
rs11605632	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12416930	0.93[ASN][1000 genomes]
rs12420456	0.88[ASN][1000 genomes]
rs12422027	0.80[ASN][1000 genomes]
rs12800339	0.80[ASN][1000 genomes]
rs17583	0.81[ASN][1000 genomes]
rs17881590	0.84[ASN][1000 genomes]
rs17886894	0.81[ASN][1000 genomes]
rs2271448	0.81[ASN][1000 genomes]
rs2277307	0.81[ASN][1000 genomes]
rs34007842	0.89[ASN][1000 genomes]
rs34281454	0.80[ASN][1000 genomes]
rs3825072	0.81[ASN][1000 genomes]
rs3953797	0.80[ASN][1000 genomes]
rs58858596	0.91[ASN][1000 genomes]
rs6591178	0.80[ASN][1000 genomes]
rs67698652	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7933509	0.80[ASN][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	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897713	chr11:64915042-65000719	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	nsv832190	chr11:64978144-65127613	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64950600-64992400	Weak transcription	Right Atrium	heart
2	chr11:64952400-64992800	Weak transcription	Fetal Heart	heart
3	chr11:64964400-64981000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:64973000-64980800	Weak transcription	NH-A	brain
5	chr11:64973800-64992600	Weak transcription	Fetal Kidney	kidney
6	chr11:64974200-64980800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:64975800-64982400	Genic enhancers	Fetal Intestine Small	intestine
8	chr11:64976600-64992600	Weak transcription	Psoas Muscle	Psoas
9	chr11:64976800-64980800	Weak transcription	Primary B cells from cord blood	blood
10	chr11:64977400-64998400	Weak transcription	Small Intestine	intestine
11	chr11:64977600-64980600	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr11:64977600-64980800	Weak transcription	GM12878-XiMat	blood
13	chr11:64977600-64993200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr11:64978000-64980800	Weak transcription	Brain Substantia Nigra	brain
15	chr11:64978200-64980800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr11:64978200-64982800	Weak transcription	Fetal Lung	lung
17	chr11:64978200-64986800	Weak transcription	HepG2	liver
18	chr11:64978400-64980800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr11:64978400-64992200	Weak transcription	Stomach Mucosa	stomach
20	chr11:64978400-64992800	Weak transcription	HSMM	muscle
21	chr11:64978600-64980800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr11:64978600-64980800	Weak transcription	Hela-S3	cervix
23	chr11:64978600-64981200	Weak transcription	Primary T cells from cord blood	blood
24	chr11:64978600-64992800	Weak transcription	HSMMtube	muscle
25	chr11:64978800-64980600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr11:64978800-64981000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:64978800-64987000	Weak transcription	NHDF-Ad	bronchial
28	chr11:64979000-64980800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr11:64979000-64980800	Weak transcription	Brain Hippocampus Middle	brain
30	chr11:64979000-64980800	Weak transcription	Dnd41	blood
31	chr11:64979000-64981600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:64979200-64981000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr11:64979200-64981000	Weak transcription	Adipose Nuclei	Adipose
34	chr11:64979200-64981000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr11:64979200-64981000	Weak transcription	Colon Smooth Muscle	Colon
36	chr11:64979200-64981000	Weak transcription	Osteobl	bone
37	chr11:64979200-64981200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:64979200-64981400	Enhancers	H1 Cell Line	embryonic stem cell
39	chr11:64979200-64983000	Weak transcription	Brain Anterior Caudate	brain
40	chr11:64979200-64983400	Enhancers	Primary hematopoietic stem cells	blood
41	chr11:64979200-64986400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr11:64979200-64987000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr11:64979200-64992400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr11:64979200-64993000	Weak transcription	Aorta	Aorta
45	chr11:64979400-64981000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr11:64979400-64981800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr11:64979400-64982200	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr11:64979400-64984400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr11:64979400-64987000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:64979400-64992400	Weak transcription	A549	lung

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