Variant report

Variant	rs7709688
Chromosome Location	chr5:76133259-76133260
allele	A/C
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	FOS	chr5:76133214-76133338	MCF10A-Er-Src	breast:	n/a	n/a
2	JUND	chr5:76133042-76133564	HCT-116	colon:	n/a	n/a
3	TCF12	chr5:76133143-76133580	SK-N-SH	brain:	n/a	n/a
4	FOS	chr5:76133159-76133466	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr5:76131046-76138228	A549	lung:	n/a	n/a
6	JUND	chr5:76133064-76133569	HCT-116	colon:	n/a	n/a
7	FOSL1	chr5:76132241-76133558	HCT-116	colon:	n/a	n/a
8	SP1	chr5:76132265-76133584	HCT-116	colon:	n/a	chr5:76132464-76132478
9	FOS	chr5:76133183-76133462	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr5:76133147-76133526	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
RN7SL208P	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10058498	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10059976	0.93[ASN][1000 genomes]
rs11952623	0.85[ASN][1000 genomes]
rs12187125	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13162638	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13173178	0.81[EUR][1000 genomes]
rs1529505	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2115499	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242995	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2243003	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2243020	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2243022	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2243026	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2243029	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2243031	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2243051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2243053	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2243057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2243059	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4380630	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs444403	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4591731	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4703719	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4704365	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6453250	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6453251	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6453253	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs66946336	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6880329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887035	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6894167	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6897362	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7703930	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv2763908	chr5:76083394-76134777	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv882210	chr5:76086597-76140337	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1025151	chr5:76086795-76134777	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3393424	chr5:76122720-76287744	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv994503	chr5:76129230-76144182	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7709688	F2RL1	cis	Whole Blood	GTEx
rs7709688	F2R	cis	Muscle Skeletal	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:76116800-76134200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:76117400-76134200	Weak transcription	Stomach Mucosa	stomach
3	chr5:76117400-76135200	Weak transcription	Colonic Mucosa	Colon
4	chr5:76118800-76134600	Weak transcription	HepG2	liver
5	chr5:76127000-76134600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:76127200-76134600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:76127400-76134200	Weak transcription	Osteobl	bone
8	chr5:76127800-76134400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:76128000-76134600	Weak transcription	Small Intestine	intestine
10	chr5:76128200-76133400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:76129200-76134800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr5:76129400-76134800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:76129600-76134600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr5:76129800-76134400	Weak transcription	NHLF	lung
15	chr5:76129800-76135800	Weak transcription	Pancreas	Pancrea
16	chr5:76130200-76134200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:76130200-76134600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr5:76130200-76134800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr5:76130200-76135800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:76130200-76137200	Weak transcription	Esophagus	oesophagus
21	chr5:76130400-76134200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:76130400-76134200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr5:76130400-76134200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:76130400-76134200	Weak transcription	Gastric	stomach
25	chr5:76130400-76134400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr5:76130400-76135600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr5:76130400-76140400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:76130600-76134200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:76130600-76134600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr5:76130800-76134800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr5:76131800-76134200	Enhancers	NH-A	brain
32	chr5:76132000-76133400	Enhancers	HUVEC	blood vessel
33	chr5:76132000-76134200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr5:76132200-76135400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:76132200-76145800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:76132400-76133400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:76132400-76133600	Genic enhancers	Fetal Intestine Small	intestine
38	chr5:76132600-76134200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:76132600-76134200	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr5:76132800-76136800	Enhancers	Fetal Intestine Large	intestine
41	chr5:76133000-76133400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:76133000-76133400	Weak transcription	Aorta	Aorta
43	chr5:76133000-76133800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr5:76133000-76134000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:76133000-76134000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:76133000-76134000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:76133000-76134000	Weak transcription	A549	lung
48	chr5:76133000-76134000	Weak transcription	Hela-S3	cervix
49	chr5:76133000-76134200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:76133000-76134200	Weak transcription	Muscle Satellite Cultured Cells	--

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