Variant report

Variant	rs11650289
Chromosome Location	chr17:45910497-45910498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:45910413-45910641	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr17:45908277-45910678	U87	brain:	n/a	n/a
3	POLR2A	chr17:45910224-45910801	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr17:45910075-45912166	HepG2	liver:	n/a	n/a
5	POLR2A	chr17:45910085-45910532	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr17:45908279-45910807	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr17:45910132-45910643	K562	blood:	n/a	n/a
8	POLR2A	chr17:45910085-45910928	HepG2	liver:	n/a	n/a
9	POLR2A	chr17:45910253-45910590	HCT-116	colon:	n/a	n/a
10	POLR2A	chr17:45910037-45910678	U87	brain:	n/a	n/a
11	POLR2A	chr17:45908290-45910588	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr17:45910334-45910650	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:45908927..45910597-chr17:45972583..45974861,2	K562	blood:
2	chr17:45910473..45912367-chr17:46035358..46036860,2	MCF-7	breast:
3	chr17:45907261..45910696-chr17:45969933..45974046,5	MCF-7	breast:
4	chr17:45894310..45903569-chr17:45906761..45911816,14	MCF-7	breast:
5	chr17:45909693..45911747-chr17:45950278..45952452,2	K562	blood:

No data

Variant related genes	Relation type
MRPL10	TF binding region
ENSG00000006025	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000264920	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1005655	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11079795	0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11079796	0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11650536	0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652439	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869958	0.90[CHB][hapmap]
rs11870002	0.91[CHB][hapmap]
rs16948401	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16948590	0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16948722	0.96[CHB][hapmap];0.91[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1985407	0.89[CHB][hapmap]
rs2074188	0.91[CHB][hapmap]
rs2074189	0.91[CHB][hapmap]
rs3809869	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs701984	0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72833426	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs878171	0.91[CHB][hapmap]
rs9674817	0.90[CHB][hapmap]

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	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv908574	chr17:45876022-45930584	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv517880	chr17:45887951-45933341	Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11650289	OSBPL7	cis	Thyroid	GTEx
rs11650289	SCRN2	cis	Whole Blood	GTEx
rs11650289	SCRN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45909200-45912800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr17:45909200-45916800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:45909400-45911800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr17:45909400-45912600	Weak transcription	HSMMtube	muscle
5	chr17:45909400-45913200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:45909400-45913200	Enhancers	Spleen	Spleen
7	chr17:45909400-45915800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr17:45909400-45917600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr17:45909600-45910600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr17:45909600-45910600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:45909600-45910600	Enhancers	Duodenum Mucosa	Duodenum
12	chr17:45909600-45910600	Enhancers	Fetal Thymus	thymus
13	chr17:45909600-45911200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr17:45909600-45911200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr17:45909600-45911200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr17:45909600-45911200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr17:45909600-45911400	Weak transcription	Left Ventricle	heart
18	chr17:45909600-45911600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr17:45909600-45911800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr17:45909600-45911800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr17:45909600-45911800	Weak transcription	HUVEC	blood vessel
22	chr17:45909600-45912200	Weak transcription	Fetal Stomach	stomach
23	chr17:45909600-45912600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr17:45909600-45912600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr17:45909600-45912600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr17:45909600-45912600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr17:45909600-45912600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr17:45909600-45912600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr17:45909600-45912600	Weak transcription	Gastric	stomach
30	chr17:45909600-45912600	Weak transcription	Right Ventricle	heart
31	chr17:45909600-45912800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr17:45909600-45912800	Weak transcription	Brain Germinal Matrix	brain
33	chr17:45909600-45912800	Weak transcription	Colonic Mucosa	Colon
34	chr17:45909600-45912800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr17:45909600-45913000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr17:45909600-45913000	Enhancers	Adipose Nuclei	Adipose
37	chr17:45909600-45913200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr17:45909600-45913200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr17:45909600-45913200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr17:45909600-45913200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr17:45909600-45913200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr17:45909600-45913200	Weak transcription	Esophagus	oesophagus
43	chr17:45909600-45913200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr17:45909600-45913200	Weak transcription	A549	lung
45	chr17:45909600-45913400	Weak transcription	Aorta	Aorta
46	chr17:45909600-45913400	Weak transcription	Ovary	ovary
47	chr17:45909600-45913400	Weak transcription	Pancreas	Pancrea
48	chr17:45909600-45913400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr17:45909600-45913400	Weak transcription	HSMM	muscle
50	chr17:45909600-45913400	Weak transcription	NHLF	lung

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