Variant report

Variant	rs6880329
Chromosome Location	chr5:76135124-76135125
allele	A/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	chr5:76134716-76135138	HCT-116	colon:	n/a	n/a
2	SP1	chr5:76134039-76135403	HCT-116	colon:	n/a	n/a
3	POLR2A	chr5:76134021-76135436	PANC-1	pancreas:	n/a	n/a
4	TCF12	chr5:76134286-76135200	SK-N-SH	brain:	n/a	n/a
5	SP1	chr5:76134020-76135446	HCT-116	colon:	n/a	n/a
6	JUND	chr5:76134727-76135319	A549	lung:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
7	JUND	chr5:76134100-76135393	HCT-116	colon:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
8	TEAD4	chr5:76134546-76135178	HCT-116	colon:	n/a	n/a
9	GATA3	chr5:76134272-76135147	SK-N-SH	brain:	n/a	chr5:76134889-76134898 chr5:76134892-76134901 chr5:76134700-76134709
10	FOSL2	chr5:76134483-76135163	A549	lung:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
11	POLR2A	chr5:76131046-76138228	A549	lung:	n/a	n/a
12	GATA3	chr5:76134173-76135207	SK-N-SH	brain:	n/a	chr5:76134889-76134898 chr5:76134892-76134901 chr5:76134700-76134709
13	PBX3	chr5:76134203-76135218	SK-N-SH	brain:	n/a	n/a
14	TEAD4	chr5:76134320-76135157	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr5:76134083-76135438	PFSK-1	brain:	n/a	n/a
16	FOSL1	chr5:76134070-76135382	HCT-116	colon:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
17	POLR2A	chr5:76134100-76135356	PANC-1	pancreas:	n/a	n/a
18	FOSL1	chr5:76134223-76135340	HCT-116	colon:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
19	POLR2A	chr5:76134017-76135348	HCT-116	colon:	n/a	n/a
20	EP300	chr5:76134836-76135177	SK-N-SH_RA	brain:	n/a	n/a
21	POLR2A	chr5:76134590-76135384	PFSK-1	brain:	n/a	n/a
22	TEAD4	chr5:76134573-76135250	HCT-116	colon:	n/a	n/a
23	JUND	chr5:76134037-76135460	HCT-116	colon:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
24	POLR2A	chr5:76135081-76135172	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
RN7SL208P	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10058498	0.91[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	0.84[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];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2115499	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242995	0.84[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];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2243020	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2243022	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2243026	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2243029	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2243031	0.83[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];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2243053	0.93[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];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2243059	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4380630	0.84[AMR][1000 genomes];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];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4703719	0.83[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	0.81[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];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6453253	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs66946336	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6887035	0.81[ASN][1000 genomes]
rs6894167	0.81[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];0.81[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];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7709688	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]

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	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	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
3	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
4	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
5	esv2762526	chr5:76134777-76153934	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6880329	F2RL1	cis	Whole Blood	GTEx
rs6880329	F2R	cis	Muscle Skeletal	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:76117400-76135200	Weak transcription	Colonic Mucosa	Colon
2	chr5:76129800-76135800	Weak transcription	Pancreas	Pancrea
3	chr5:76130200-76135800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:76130200-76137200	Weak transcription	Esophagus	oesophagus
5	chr5:76130400-76135600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr5:76130400-76140400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:76132200-76135400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:76132200-76145800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:76132800-76136800	Enhancers	Fetal Intestine Large	intestine
10	chr5:76133600-76136800	Enhancers	Fetal Intestine Small	intestine
11	chr5:76133800-76135200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:76133800-76135200	Enhancers	HUVEC	blood vessel
13	chr5:76134000-76135200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:76134000-76135200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:76134000-76136000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:76134000-76136000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:76134200-76135200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:76134200-76135200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr5:76134200-76135200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:76134200-76135200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr5:76134200-76135200	Enhancers	Stomach Mucosa	stomach
22	chr5:76134200-76135400	Enhancers	NHDF-Ad	bronchial
23	chr5:76134200-76135400	Enhancers	Osteobl	bone
24	chr5:76134200-76135800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:76134200-76136000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr5:76134200-76136000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr5:76134200-76136200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:76134200-76136800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr5:76134400-76135200	Flanking Active TSS	Hela-S3	cervix
30	chr5:76134400-76135200	Enhancers	NHLF	lung
31	chr5:76134400-76135400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:76134400-76135400	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr5:76134600-76135400	Enhancers	H1 Cell Line	embryonic stem cell
34	chr5:76134600-76136400	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr5:76134800-76135200	Flanking Active TSS	A549	lung
36	chr5:76134800-76135400	Enhancers	Duodenum Mucosa	Duodenum
37	chr5:76134800-76135400	Enhancers	Gastric	stomach
38	chr5:76134800-76135400	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr5:76134800-76136000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:76134800-76136000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr5:76135000-76135400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:76135000-76135400	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr5:76135000-76135400	Enhancers	NH-A	brain
44	chr5:76135000-76136000	Weak transcription	Fetal Kidney	kidney
45	chr5:76135000-76136400	Weak transcription	HepG2	liver
46	chr5:76135000-76137200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:76135000-76138600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr5:76135000-76139800	Weak transcription	Small Intestine	intestine

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