Variant report

Variant	rs3808056
Chromosome Location	chr7:127681731-127681732
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	JUND	chr7:127681111-127681777	SK-N-SH	brain:	n/a	chr7:127681424-127681434 chr7:127681425-127681433 chr7:127681546-127681560 chr7:127681423-127681434 chr7:127681421-127681432 chr7:127681426-127681433 chr7:127681425-127681434 chr7:127681423-127681435
2	NFIC	chr7:127681222-127681739	SK-N-SH	brain:	n/a	chr7:127681451-127681468
3	GATA3	chr7:127681180-127681874	SK-N-SH	brain:	n/a	chr7:127681669-127681676
4	NFIC	chr7:127681098-127681897	SK-N-SH	brain:	n/a	chr7:127681451-127681468
5	FOSL2	chr7:127681230-127681741	SK-N-SH	brain:	n/a	chr7:127681424-127681434 chr7:127681425-127681433 chr7:127681546-127681560 chr7:127681421-127681432 chr7:127681426-127681433 chr7:127681425-127681434 chr7:127681423-127681435
6	GATA3	chr7:127681091-127681898	SK-N-SH	brain:	n/a	chr7:127681669-127681676
7	JUND	chr7:127680647-127683412	SK-N-SH	brain:	n/a	chr7:127681424-127681434 chr7:127681425-127681433 chr7:127681546-127681560 chr7:127681423-127681434 chr7:127680891-127680900 chr7:127682140-127682152 chr7:127681421-127681432 chr7:127681426-127681433 chr7:127681425-127681434 chr7:127682983-127682992 chr7:127681423-127681435
8	TCF12	chr7:127681108-127681809	SK-N-SH	brain:	n/a	n/a
9	FOSL2	chr7:127681140-127681824	SK-N-SH	brain:	n/a	chr7:127681424-127681434 chr7:127681425-127681433 chr7:127681546-127681560 chr7:127681421-127681432 chr7:127681426-127681433 chr7:127681425-127681434 chr7:127681423-127681435
10	NFIC	chr7:127681196-127681737	ECC-1	luminal epithelium:	n/a	chr7:127681451-127681468

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:127679314..127682339-chr7:127683889..127685998,3	K562	blood:

Variant related genes	Relation type
SND1	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1024910	0.92[EUR][1000 genomes]
rs1193333	0.91[EUR][1000 genomes]
rs1193335	0.91[EUR][1000 genomes]
rs1193336	0.89[ASN][1000 genomes]
rs124756	0.84[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs1345509	0.85[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs1419968	0.88[JPT][hapmap]
rs17151567	0.82[LWK][hapmap]
rs178734	0.91[ASN][1000 genomes]
rs2241291	0.88[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs225241	0.91[ASN][1000 genomes]
rs2543477	0.88[EUR][1000 genomes]
rs322813	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs322819	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs322820	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs322821	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs322822	0.80[EUR][1000 genomes]
rs322823	0.84[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap]
rs322824	0.80[EUR][1000 genomes]
rs322825	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap]
rs322826	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs322827	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs322828	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs322831	0.89[ASN][1000 genomes]
rs322834	0.91[ASN][1000 genomes]
rs322835	0.89[ASN][1000 genomes]
rs322836	0.89[ASN][1000 genomes]
rs322838	0.89[ASN][1000 genomes]
rs322840	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs35774036	0.88[ASN][1000 genomes]
rs3757755	0.92[ASN][1000 genomes]
rs3757759	0.81[EUR][1000 genomes]
rs3757760	0.88[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs3757763	0.88[CEU][hapmap];0.80[CHB][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs3779523	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs3779526	0.85[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3779527	0.92[EUR][1000 genomes]
rs3808061	0.82[ASN][1000 genomes]
rs3808077	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs3808078	0.81[EUR][1000 genomes]
rs3808086	0.80[EUR][1000 genomes]
rs3808088	0.81[CEU][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs3823995	0.85[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4728082	0.82[LWK][hapmap]
rs4731390	0.82[LWK][hapmap]
rs62481443	0.80[EUR][1000 genomes]
rs62481447	0.80[EUR][1000 genomes]
rs62481450	0.81[EUR][1000 genomes]
rs6467154	0.82[LWK][hapmap]
rs6467155	0.92[EUR][1000 genomes]
rs6467156	0.92[EUR][1000 genomes]
rs6944446	0.80[CHB][hapmap]
rs6969233	0.82[EUR][1000 genomes]
rs6972847	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6973092	0.85[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7789322	0.91[EUR][1000 genomes]
rs9791922	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3808056	GCC1	cis	lymphoblastoid	seeQTL
rs3808056	GPR37	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127645000-127684000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:127669400-127726600	Weak transcription	Hela-S3	cervix
3	chr7:127669600-127718200	Weak transcription	A549	lung
4	chr7:127670400-127698800	Weak transcription	Dnd41	blood
5	chr7:127672600-127695400	Weak transcription	Aorta	Aorta
6	chr7:127672800-127682200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr7:127673000-127681800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr7:127673000-127692600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr7:127673000-127692800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr7:127673000-127697800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr7:127673200-127681800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:127673200-127682400	Weak transcription	Lung	lung
13	chr7:127673200-127682400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr7:127673200-127684000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr7:127673200-127684800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr7:127673200-127692600	Weak transcription	Right Atrium	heart
17	chr7:127673200-127712000	Weak transcription	Esophagus	oesophagus
18	chr7:127673400-127682200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:127673400-127682400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:127673400-127682400	Weak transcription	Placenta	Placenta
21	chr7:127673400-127684000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr7:127673400-127684000	Weak transcription	Left Ventricle	heart
23	chr7:127673600-127681800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr7:127673600-127682400	Weak transcription	Spleen	Spleen
25	chr7:127673600-127692200	Weak transcription	Adipose Nuclei	Adipose
26	chr7:127673600-127692200	Weak transcription	Fetal Muscle Leg	muscle
27	chr7:127673600-127692200	Weak transcription	Gastric	stomach
28	chr7:127673800-127682000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr7:127673800-127703400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr7:127673800-127715400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr7:127674200-127682600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:127674600-127682200	Weak transcription	Primary T cells from cord blood	blood
33	chr7:127674600-127692200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr7:127674800-127682200	Weak transcription	K562	blood
35	chr7:127675000-127681800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:127675000-127685400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:127675200-127692200	Weak transcription	Pancreas	Pancrea
38	chr7:127675200-127695200	Weak transcription	Psoas Muscle	Psoas
39	chr7:127675400-127682200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr7:127675800-127682000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr7:127675800-127692800	Weak transcription	Fetal Lung	lung
42	chr7:127676600-127685600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr7:127677000-127682000	Weak transcription	Fetal Stomach	stomach
44	chr7:127677600-127682000	Weak transcription	Colonic Mucosa	Colon
45	chr7:127678000-127701200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr7:127678200-127682400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr7:127679200-127682000	Weak transcription	Liver	Liver
48	chr7:127679200-127682200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr7:127679600-127682400	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr7:127679600-127684000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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