Variant report

Variant	rs11652827
Chromosome Location	chr17:46012505-46012506
allele	C/T
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	chr17:46012221-46012615	U87	brain:	n/a	n/a
2	POLR2A	chr17:46012089-46012666	U87	brain:	n/a	n/a
3	FOS	chr17:46012240-46012674	HUVEC	blood vessel:	n/a	chr17:46012522-46012532 chr17:46012522-46012532 chr17:46012579-46012588 chr17:46012360-46012369 chr17:46012523-46012531 chr17:46012522-46012532
4	ELF1	chr17:46012248-46012651	K562	blood:	n/a	chr17:46012439-46012452
5	POLR2A	chr17:46012221-46012655	U87	brain:	n/a	n/a
6	POLR2A	chr17:46012318-46012527	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46005896..46008732-chr17:46011956..46013614,2	K562	blood:
2	chr17:45977677..45979429-chr17:46010688..46013383,2	MCF-7	breast:
3	chr17:46012053..46013747-chr17:46016298..46020138,4	MCF-7	breast:
4	chr17:46010778..46013733-chr5:72250921..72253254,2	MCF-7	breast:
5	chr17:45972283..45976323-chr17:46012255..46015718,3	MCF-7	breast:
6	chr17:45985712..45987886-chr17:46012163..46013782,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266601	TF binding region
ENSG00000234494	Chromatin interaction
ENSG00000157107	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000272081	Chromatin interaction
ENSG00000108439	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10459927	0.84[ASN][1000 genomes]
rs11079801	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11079803	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1108833	0.86[ASN][1000 genomes]
rs1130932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652185	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11655068	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11655352	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11659126	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870852	0.86[ASN][1000 genomes]
rs12601827	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12602494	0.85[ASN][1000 genomes]
rs12939739	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228251	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2228253	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2229358	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2318118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2325747	0.89[ASN][1000 genomes]
rs2325751	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525107	0.81[ASN][1000 genomes]
rs3096	0.85[ASN][1000 genomes]
rs34593510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35280206	0.85[ASN][1000 genomes]
rs36124074	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764396	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4369725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793731	0.85[ASN][1000 genomes]
rs4793732	0.81[ASN][1000 genomes]
rs4793733	0.85[ASN][1000 genomes]
rs4793737	0.85[ASN][1000 genomes]
rs4794261	0.86[ASN][1000 genomes]
rs4794286	0.89[ASN][1000 genomes]
rs4794332	0.85[ASN][1000 genomes]
rs6503934	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67194241	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208707	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7211859	0.86[ASN][1000 genomes]
rs72840237	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8066893	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8071003	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9895863	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903223	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv2072	chr17:45998637-46019626	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11652827	RP11-6N17.4	cis	Muscle Skeletal	GTEx
rs11652827	SP2	Cis_1M	lymphoblastoid	RTeQTL
rs11652827	RP11-6N17.4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45983200-46018200	Weak transcription	Fetal Brain Male	brain
2	chr17:45993800-46017400	Weak transcription	Psoas Muscle	Psoas
3	chr17:45994000-46013200	Weak transcription	Fetal Heart	heart
4	chr17:45996200-46012600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:45999200-46018200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr17:46002400-46013400	Weak transcription	Stomach Mucosa	stomach
7	chr17:46003200-46014200	Weak transcription	GM12878-XiMat	blood
8	chr17:46003200-46018400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:46004400-46012600	Weak transcription	Hela-S3	cervix
10	chr17:46004600-46013200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr17:46004600-46018200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr17:46005400-46017400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:46005400-46018200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr17:46006200-46017800	Weak transcription	Small Intestine	intestine
15	chr17:46006600-46013400	Weak transcription	Right Atrium	heart
16	chr17:46006800-46015600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr17:46007000-46015600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:46007000-46018200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr17:46007000-46018400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr17:46007200-46018200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr17:46007600-46013200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr17:46007600-46017400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr17:46007600-46018200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr17:46007600-46018600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:46007800-46018200	Weak transcription	Colonic Mucosa	Colon
26	chr17:46007800-46018400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr17:46007800-46018800	Weak transcription	Gastric	stomach
28	chr17:46008000-46013200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr17:46008000-46013200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr17:46008000-46015400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr17:46008000-46015400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr17:46008000-46015400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr17:46008000-46015600	Weak transcription	Adipose Nuclei	Adipose
34	chr17:46008000-46015800	Weak transcription	Brain Hippocampus Middle	brain
35	chr17:46008000-46018200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr17:46008000-46018200	Weak transcription	Fetal Intestine Large	intestine
37	chr17:46008000-46018200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr17:46008000-46018400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr17:46008000-46018400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr17:46008200-46013400	Weak transcription	Left Ventricle	heart
41	chr17:46008200-46013600	Weak transcription	Esophagus	oesophagus
42	chr17:46008200-46015400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr17:46008200-46015600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr17:46008200-46015800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr17:46008200-46017400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr17:46008200-46017400	Weak transcription	Pancreas	Pancrea
47	chr17:46008200-46017600	Weak transcription	Liver	Liver
48	chr17:46008200-46017600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr17:46008200-46017600	Weak transcription	Ovary	ovary
50	chr17:46008200-46017600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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