Variant report

Variant	rs6953134
Chromosome Location	chr7:127350568-127350569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127348829..127352435-chr7:127355750..127359950,4	K562	blood:
2	chr7:127350301..127352881-chr7:127354512..127357487,2	MCF-7	breast:
3	chr7:127349398..127351131-chr7:127431293..127433325,2	K562	blood:
4	chr7:127349984..127350918-chr7:127849791..127850455,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197157	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10229165	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10229583	1.00[CHB][hapmap]
rs10238047	0.93[EUR][1000 genomes]
rs10239440	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10249616	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10265516	0.90[ASN][1000 genomes]
rs10270127	0.94[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes]
rs10280863	0.90[ASN][1000 genomes]
rs11765620	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11767317	0.97[ASN][1000 genomes]
rs11773160	0.93[ASN][1000 genomes]
rs1440971	0.93[EUR][1000 genomes]
rs1440972	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808089	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4473953	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57103099	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6467152	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6943219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[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];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6946292	0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6947779	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6965698	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6969353	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6976887	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6979634	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	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7778413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7781189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs7783102	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7783478	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7784200	0.88[ASW][hapmap];0.88[CHB][hapmap]
rs7786786	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7792695	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7801118	0.87[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];0.87[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	nsv1030387	chr7:127348973-127455890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6953134	C7orf54	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127324800-127350800	Weak transcription	Fetal Brain Female	brain
2	chr7:127324800-127372200	Weak transcription	Fetal Heart	heart
3	chr7:127325600-127363000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:127326000-127352200	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr7:127326000-127354400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:127326000-127355600	Strong transcription	Duodenum Mucosa	Duodenum
7	chr7:127326200-127350600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:127326400-127350800	Strong transcription	Primary B cells from cord blood	blood
9	chr7:127326400-127350800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr7:127326400-127351000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr7:127326400-127351800	Strong transcription	Placenta	Placenta
12	chr7:127326400-127352800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:127326400-127356600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr7:127326600-127351000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr7:127326600-127355200	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr7:127326600-127379800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr7:127326800-127371000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:127327000-127355200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:127330000-127355600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr7:127331000-127350600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:127331600-127375600	Strong transcription	Fetal Thymus	thymus
22	chr7:127332600-127351000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr7:127333200-127351000	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:127333400-127351800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr7:127333600-127350800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr7:127333800-127351800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr7:127333800-127354200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr7:127334200-127350800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:127334200-127351000	Strong transcription	Liver	Liver
30	chr7:127334200-127351600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr7:127334400-127376600	Weak transcription	Fetal Brain Male	brain
32	chr7:127334600-127350800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr7:127334600-127350800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:127334600-127351000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:127334600-127354400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr7:127335000-127351200	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr7:127335000-127359400	Strong transcription	Hela-S3	cervix
38	chr7:127337400-127350800	Strong transcription	Fetal Muscle Leg	muscle
39	chr7:127339000-127357400	Weak transcription	Small Intestine	intestine
40	chr7:127339400-127371000	Weak transcription	Right Atrium	heart
41	chr7:127340600-127351200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr7:127341200-127350800	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr7:127341800-127353400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr7:127342600-127350800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr7:127342600-127351600	Strong transcription	Fetal Kidney	kidney
46	chr7:127344600-127353200	Weak transcription	Brain Angular Gyrus	brain
47	chr7:127344600-127371200	Weak transcription	Brain Germinal Matrix	brain
48	chr7:127345000-127350800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr7:127345000-127362000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr7:127345200-127351000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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