Variant report

Variant	rs2071825
Chromosome Location	chr6:117862048-117862049
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	CEBPB	chr6:117861938-117862364	HCT-116	colon:	n/a	n/a
2	FOSL2	chr6:117861945-117862236	A549	lung:	n/a	n/a
3	FOS	chr6:117861737-117862338	MCF10A-Er-Src	breast:	n/a	chr6:117861815-117861824
4	STAT3	chr6:117861838-117862278	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr6:117861844-117862284	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr6:117861977-117862270	HepG2	liver:	n/a	n/a
7	MYC	chr6:117861840-117862249	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr6:117861604-117862340	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr6:117861865-117862300	A549	lung:	n/a	n/a
10	MYC	chr6:117861745-117862280	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr6:117861801-117862348	A549	lung:	n/a	n/a
12	POLR2A	chr6:117861980-117862333	MCF10A-Er-Src	breast:	n/a	n/a
13	CEBPB	chr6:117861880-117862270	IMR90	lung:	n/a	n/a
14	E2F4	chr6:117861926-117862170	MCF10A-Er-Src	breast:	n/a	n/a
15	CEBPB	chr6:117861780-117862277	HCT-116	colon:	n/a	n/a
16	FOS	chr6:117861862-117862350	MCF10A-Er-Src	breast:	n/a	n/a
17	STAT3	chr6:117861819-117862356	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr6:117861899-117862083	SK-N-SH	brain:	n/a	n/a
19	CEBPB	chr6:117861913-117862250	Hela-S3	cervix:	n/a	n/a
20	CEBPB	chr6:117861816-117862286	A549	lung:	n/a	n/a
21	STAT3	chr6:117861771-117862580	MCF10A-Er-Src	breast:	n/a	n/a
22	FOS	chr6:117861763-117862343	MCF10A-Er-Src	breast:	n/a	chr6:117861815-117861824
23	FOSL2	chr6:117861792-117862331	A549	lung:	n/a	chr6:117861815-117861824

Variant related genes	Relation type
DCBLD1	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10457315	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457318	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10872153	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11153672	0.94[JPT][hapmap]
rs12205963	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1501474	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs1532680	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1759	0.96[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1967193	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1967194	0.83[EUR][1000 genomes]
rs2062663	0.85[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2088870	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs210617	0.87[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210619	0.82[CEU][hapmap]
rs210630	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs210633	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs210637	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs210639	0.96[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs210642	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3752848	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4946265	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946267	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4946269	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4946273	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67663020	0.82[EUR][1000 genomes]
rs9285425	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285426	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs9320609	0.82[CEU][hapmap]
rs9320612	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9320614	0.82[EUR][1000 genomes]
rs9320616	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9320617	0.84[EUR][1000 genomes]
rs9374671	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9374674	0.84[EUR][1000 genomes]
rs9387491	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9401014	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9401019	0.83[EUR][1000 genomes]
rs9401023	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9489217	0.82[CEU][hapmap]
rs9489223	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9489238	0.81[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs9765895	0.80[EUR][1000 genomes]
rs9767060	0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2071825	GJA1	cis	parietal	SCAN
rs2071825	DSE	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117819800-117868800	Weak transcription	Spleen	Spleen
2	chr6:117821600-117868800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:117823200-117868800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:117823200-117869600	Weak transcription	Small Intestine	intestine
5	chr6:117828000-117866200	Weak transcription	Esophagus	oesophagus
6	chr6:117834400-117863600	Weak transcription	Gastric	stomach
7	chr6:117835200-117868800	Weak transcription	Colonic Mucosa	Colon
8	chr6:117835400-117868800	Weak transcription	Psoas Muscle	Psoas
9	chr6:117836600-117869600	Weak transcription	Stomach Mucosa	stomach
10	chr6:117838600-117869000	Weak transcription	Ovary	ovary
11	chr6:117842800-117866200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:117845200-117866200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:117845800-117868800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:117846800-117869600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:117851800-117868800	Weak transcription	Right Ventricle	heart
16	chr6:117852800-117863600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:117852800-117867800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:117853200-117862600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:117853200-117868600	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr6:117853200-117868600	Strong transcription	HSMM	muscle
21	chr6:117853400-117868800	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:117853400-117868800	Weak transcription	NHDF-Ad	bronchial
23	chr6:117853600-117868600	Strong transcription	Osteobl	bone
24	chr6:117853600-117868800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:117854200-117868800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr6:117854400-117868800	Weak transcription	Brain Angular Gyrus	brain
27	chr6:117855000-117868200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:117857000-117869200	Weak transcription	Fetal Kidney	kidney
29	chr6:117857600-117862400	Strong transcription	NHLF	lung
30	chr6:117857800-117867600	Weak transcription	Hela-S3	cervix
31	chr6:117857800-117868600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:117858000-117867600	Weak transcription	HSMMtube	muscle
33	chr6:117858000-117868800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:117858000-117869200	Weak transcription	Placenta	Placenta
35	chr6:117858200-117865200	Weak transcription	K562	blood
36	chr6:117858200-117866000	Strong transcription	NH-A	brain
37	chr6:117858200-117870400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:117858400-117865200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:117858400-117865800	Weak transcription	Aorta	Aorta
40	chr6:117859000-117866200	Strong transcription	HUVEC	blood vessel
41	chr6:117859000-117868800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr6:117859200-117862600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:117859200-117862800	Strong transcription	Liver	Liver
44	chr6:117859400-117862600	Strong transcription	Adipose Nuclei	Adipose
45	chr6:117859400-117868800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:117859400-117868800	Weak transcription	Brain Anterior Caudate	brain
47	chr6:117859600-117862600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr6:117859600-117868600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr6:117859800-117862400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr6:117859800-117862800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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