Variant report

Variant	rs6979634
Chromosome Location	chr7:127323965-127323966
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	WRNIP1	chr7:127323955-127324319	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:127323537-127324432	HepG2	liver:	n/a	n/a
3	EBF1	chr7:127323929-127324709	GM12878	blood:	n/a	chr7:127324333-127324342 chr7:127324331-127324344 chr7:127324083-127324096 chr7:127324085-127324094 chr7:127324085-127324094 chr7:127324084-127324094 chr7:127324331-127324342 chr7:127324332-127324342

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:127322349..127324124-chr7:127326869..127328716,2	MCF-7	breast:
2	chr7:127321239..127323993-chr7:127348040..127350478,2	K562	blood:

Variant related genes	Relation type
SND1	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10229165	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10229583	1.00[CHB][hapmap]
rs10238047	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10239440	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10249616	0.80[EUR][1000 genomes]
rs10265516	0.85[AFR][1000 genomes]
rs10270127	0.94[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes]
rs11765620	0.80[EUR][1000 genomes]
rs1440971	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1440972	0.80[EUR][1000 genomes]
rs3808089	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.82[YRI][hapmap]
rs4473953	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.82[YRI][hapmap]
rs6467152	0.82[EUR][1000 genomes]
rs6943219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6943385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6946292	0.81[AMR][1000 genomes]
rs6947779	0.82[EUR][1000 genomes]
rs6953134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73450923	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7778413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7781189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7783102	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.82[YRI][hapmap]
rs7783478	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7784200	0.88[CHB][hapmap]
rs7786786	0.81[ASN][1000 genomes]
rs7792695	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7801118	0.90[EUR][1000 genomes]
rs806176	0.83[CHB][hapmap]
rs806178	0.83[CHB][hapmap]
rs806179	0.94[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831122	chr7:127143207-127357885	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv1031658	chr7:127266882-127376775	Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv831123	chr7:127289511-127510396	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv981781	chr7:127322449-127326404	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6979634	C7orf54	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127293200-127326600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr7:127294800-127327400	Weak transcription	Fetal Kidney	kidney
3	chr7:127295400-127326400	Weak transcription	Thymus	Thymus
4	chr7:127296200-127326600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr7:127299000-127334400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr7:127304600-127326600	Weak transcription	Fetal Stomach	stomach
7	chr7:127305200-127326600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:127307000-127324200	Weak transcription	Fetal Heart	heart
9	chr7:127307000-127324200	Weak transcription	Stomach Mucosa	stomach
10	chr7:127307000-127330200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:127307800-127324400	Weak transcription	Small Intestine	intestine
12	chr7:127308200-127326600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr7:127308400-127326600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr7:127308800-127333600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:127309400-127333600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:127309600-127339600	Weak transcription	Brain Germinal Matrix	brain
17	chr7:127310600-127326400	Weak transcription	Fetal Muscle Leg	muscle
18	chr7:127311200-127326600	Weak transcription	Hela-S3	cervix
19	chr7:127314400-127326000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr7:127314400-127326600	Weak transcription	Spleen	Spleen
21	chr7:127314400-127327600	Weak transcription	Brain Anterior Caudate	brain
22	chr7:127314400-127330400	Weak transcription	Esophagus	oesophagus
23	chr7:127316400-127326600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr7:127317000-127326600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr7:127318200-127325800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:127318200-127333800	Weak transcription	Brain Angular Gyrus	brain
27	chr7:127318600-127326200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr7:127319200-127324000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:127319200-127326200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr7:127319200-127326200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr7:127319200-127326400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:127319200-127326600	Weak transcription	Lung	lung
33	chr7:127319200-127326600	Weak transcription	HSMM	muscle
34	chr7:127319200-127330400	Weak transcription	Aorta	Aorta
35	chr7:127319400-127324000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr7:127319400-127324200	Weak transcription	NH-A	brain
37	chr7:127319400-127326200	Weak transcription	Fetal Thymus	thymus
38	chr7:127319400-127327000	Weak transcription	A549	lung
39	chr7:127319800-127326400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr7:127319800-127328200	Weak transcription	HSMMtube	muscle
41	chr7:127320000-127324400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr7:127320000-127325800	Weak transcription	Primary T cells from cord blood	blood
43	chr7:127320000-127326000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr7:127320000-127326400	Weak transcription	Dnd41	blood
45	chr7:127320000-127326600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr7:127320000-127326800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr7:127320000-127326800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr7:127320000-127330400	Weak transcription	Colon Smooth Muscle	Colon
49	chr7:127320200-127326400	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr7:127320400-127329600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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