Variant report

Variant	rs11204666
Chromosome Location	chr1:150543128-150543129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:61 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:150541941-150543415	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr1:150541934-150543193	MCF-7	breast:	n/a	n/a
3	POLR2A	chr1:150538698-150546656	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:150538889-150552727	K562	blood:	n/a	n/a
5	POLR2A	chr1:150538866-150546573	U87	brain:	n/a	n/a
6	POLR2A	chr1:150539774-150546448	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr1:150542374-150543131	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr1:150541963-150546408	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr1:150527732-150552686	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr1:150530622-150553130	IMR90	lung:	n/a	n/a
11	POLR2A	chr1:150542076-150543152	GM12891	blood:	n/a	n/a
12	POLR2A	chr1:150540216-150546538	U87	brain:	n/a	n/a
13	POLR2A	chr1:150538654-150552953	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:150539727-150546572	HepG2	liver:	n/a	n/a
15	MYC	chr1:150542036-150543187	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr1:150530539-150552850	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr1:150542033-150543340	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:150538736-150552926	GM12878	blood:	n/a	n/a
19	ZNF384	chr1:150542782-150543199	K562	blood:	n/a	n/a
20	POLR2A	chr1:150538866-150553173	U87	brain:	n/a	n/a
21	POLR2A	chr1:150540609-150543144	K562	blood:	n/a	n/a
22	POLR2A	chr1:150538945-150546560	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr1:150542833-150544015	ECC-1	luminal epithelium:	n/a	n/a
24	MTA3	chr1:150542428-150543382	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:150542302-150546578	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr1:150538877-150553278	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:150538822-150553196	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr1:150542184-150543203	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr1:150539636-150544211	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr1:150542018-150543414	K562	blood:	n/a	n/a
31	POLR2A	chr1:150542706-150546537	K562	blood:	n/a	n/a
32	POLR2A	chr1:150542040-150546487	GM12891	blood:	n/a	n/a
33	POLR2A	chr1:150541942-150546679	GM12891	blood:	n/a	n/a
34	POLR2A	chr1:150541930-150546677	GM12891	blood:	n/a	n/a
35	POLR2A	chr1:150538740-150553070	K562	blood:	n/a	n/a
36	POLR2A	chr1:150538874-150549135	GM12878	blood:	n/a	n/a
37	MYC	chr1:150541722-150543456	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr1:150538937-150546714	GM12892	blood:	n/a	n/a
39	POLR2A	chr1:150538892-150546716	GM12892	blood:	n/a	n/a
40	POLR2A	chr1:150542173-150543226	GM19099	blood:	n/a	n/a
41	POLR2A	chr1:150538916-150552586	K562	blood:	n/a	n/a
42	POLR2A	chr1:150542443-150543970	HepG2	liver:	n/a	n/a
43	POLR2A	chr1:150539734-150546272	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr1:150542045-150546562	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:150542073-150543222	H1-hESC	embryonic stem cell:	n/a	n/a
46	ZMIZ1	chr1:150543020-150543197	K562	blood:	n/a	n/a
47	POLR2A	chr1:150542037-150544067	GM12892	blood:	n/a	n/a
48	POLR2A	chr1:150542014-150553018	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr1:150531141-150552175	A549	lung:	n/a	n/a
50	POLR2A	chr1:150541798-150544263	U87	brain:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150541646..150543170-chr22:29209298..29211232,2	MCF-7	breast:
2	chr1:150541068..150543628-chr1:150783525..150786883,3	MCF-7	breast:
3	chr1:150541344..150544160-chr1:150572544..150574410,2	K562	blood:
4	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
5	chr1:150542528..150547161-chr1:150576124..150579510,4	K562	blood:
6	chr1:150542533..150544635-chr1:150845972..150847579,2	MCF-7	breast:
7	chr1:150486114..150488258-chr1:150542189..150544516,3	K562	blood:
8	chr1:150542198..150544708-chr1:150893350..150895206,2	K562	blood:
9	chr1:150542997..150546031-chr1:150978720..150981188,4	MCF-7	breast:
10	chr1:150541549..150544184-chr1:150897269..150900025,2	K562	blood:
11	chr1:150542073..150543694-chr1:150971121..150973103,2	K562	blood:

No data

Variant related genes	Relation type
RN7SL600P	TF binding region
RN7SL473P	TF binding region
ENSG00000143363	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000228126	Chromatin interaction
ENSG00000253047	Chromatin interaction
ENSG00000143420	Chromatin interaction
ENSG00000272858	Chromatin interaction
ENSG00000200175	Chromatin interaction
ENSG00000143379	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11204671	0.82[ASN][1000 genomes]
rs17649760	1.00[ASW][hapmap]
rs35967040	0.81[ASN][1000 genomes]
rs6587756	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs6655975	0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7549723	0.85[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	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
3	nsv535156	chr1:150540117-150575941	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11204666	TNFAIP8L2	cis	cerebellum	SCAN
rs11204666	HORMAD1	cis	Nerve Tibial	GTEx
rs11204666	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs11204666	HORMAD1	cis	parietal	SCAN
rs11204666	HIST2H2AC	cis	cerebellum	SCAN
rs11204666	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs11204666	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs11204666	CTSS	cis	cerebellum	SCAN
rs11204666	GOLPH3L	cis	Nerve Tibial	GTEx
rs11204666	ADAMTSL4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150534400-150547200	Weak transcription	Ovary	ovary
2	chr1:150538800-150543800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr1:150538800-150543800	Enhancers	HMEC	breast
4	chr1:150539800-150543400	Weak transcription	Gastric	stomach
5	chr1:150540200-150543200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:150540600-150543400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
7	chr1:150540600-150543600	Enhancers	Pancreas	Pancrea
8	chr1:150540600-150544200	Enhancers	NHLF	lung
9	chr1:150540600-150544800	Enhancers	Psoas Muscle	Psoas
10	chr1:150540800-150543400	Enhancers	Colonic Mucosa	Colon
11	chr1:150540800-150543600	Enhancers	HUVEC	blood vessel
12	chr1:150540800-150543800	Enhancers	NHDF-Ad	bronchial
13	chr1:150540800-150545600	Enhancers	Right Atrium	heart
14	chr1:150540800-150545600	Enhancers	Right Ventricle	heart
15	chr1:150541000-150543200	Enhancers	Left Ventricle	heart
16	chr1:150541000-150543400	Enhancers	Brain Hippocampus Middle	brain
17	chr1:150541200-150543400	Enhancers	Osteobl	bone
18	chr1:150541400-150543800	Enhancers	NHEK	skin
19	chr1:150541400-150544200	Enhancers	Fetal Heart	heart
20	chr1:150541400-150545400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:150541400-150545600	Genic enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:150541400-150545800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:150541400-150547200	Genic enhancers	Fetal Intestine Small	intestine
24	chr1:150541400-150549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:150541600-150543200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr1:150541600-150543200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr1:150541600-150543200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:150541600-150543200	Enhancers	A549	lung
29	chr1:150541600-150543200	Enhancers	HSMMtube	muscle
30	chr1:150541600-150543600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:150541600-150543600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:150541600-150543600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr1:150541600-150543600	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr1:150541600-150543600	Enhancers	Dnd41	blood
35	chr1:150541600-150543800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:150541600-150543800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:150541600-150544000	Enhancers	Colon Smooth Muscle	Colon
38	chr1:150541600-150544400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr1:150541600-150545200	Weak transcription	Fetal Kidney	kidney
40	chr1:150541600-150545600	Weak transcription	Brain Angular Gyrus	brain
41	chr1:150541800-150543600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:150541800-150544400	Genic enhancers	Fetal Muscle Trunk	muscle
43	chr1:150541800-150544600	Genic enhancers	Primary T cells fromperipheralblood	blood
44	chr1:150541800-150546800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:150542000-150544000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
46	chr1:150542000-150545400	Genic enhancers	Primary B cells from peripheral blood	blood
47	chr1:150542000-150545600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:150542000-150545600	Strong transcription	Fetal Brain Female	brain
49	chr1:150542000-150547200	Genic enhancers	Primary monocytes fromperipheralblood	blood
50	chr1:150542200-150543200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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