Variant report

Variant	rs6943385
Chromosome Location	chr7:127308428-127308429
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:127290530..127295026-chr7:127301648..127308446,12	MCF-7	breast:
2	chr7:127289933..127293369-chr7:127304978..127309849,8	MCF-7	breast:
3	chr7:127304778..127307957-chr7:127308207..127312906,6	K562	blood:
4	chr7:127306084..127308434-chr7:127323549..127326082,2	K562	blood:
5	chr7:127305089..127308813-chr7:127315948..127319182,5	K562	blood:
6	chr7:127306135..127308740-chr7:127475843..127478656,2	K562	blood:
7	chr7:127295122..127296955-chr7:127306718..127309391,2	MCF-7	breast:
8	chr7:127308000..127310358-chr7:127310705..127312851,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197157	Chromatin interaction
ENSG00000240790	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10229165	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10229583	1.00[CHB][hapmap]
rs10238047	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10239440	0.80[EUR][1000 genomes]
rs10265516	0.83[ASN][1000 genomes]
rs10270127	0.94[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes]
rs10280863	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11765620	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11767317	0.81[ASN][1000 genomes]
rs1440971	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1440972	0.84[ASN][1000 genomes]
rs3808089	0.83[ASN][1000 genomes]
rs4473953	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap]
rs57103099	0.83[ASN][1000 genomes]
rs6467152	0.80[EUR][1000 genomes];0.81[ASN][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];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947779	0.83[ASN][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];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6965698	0.80[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];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73450923	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7781189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7783102	0.83[ASN][1000 genomes]
rs7783478	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784200	0.88[CHB][hapmap]
rs7786786	0.85[ASN][1000 genomes]
rs7792695	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7801118	0.92[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];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6943385	C7orf54	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127293200-127322000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:127293200-127326600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:127294800-127327400	Weak transcription	Fetal Kidney	kidney
4	chr7:127295000-127314000	Weak transcription	Colon Smooth Muscle	Colon
5	chr7:127295000-127314000	Weak transcription	Ovary	ovary
6	chr7:127295000-127314000	Weak transcription	Spleen	Spleen
7	chr7:127295000-127315600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr7:127295000-127318400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:127295000-127322200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr7:127295200-127317800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr7:127295200-127321800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr7:127295400-127326400	Weak transcription	Thymus	Thymus
13	chr7:127296000-127308800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:127296200-127309200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr7:127296200-127318200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr7:127296200-127326600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr7:127296600-127308800	Weak transcription	Right Atrium	heart
18	chr7:127296600-127314000	Weak transcription	Lung	lung
19	chr7:127296600-127314000	Weak transcription	Right Ventricle	heart
20	chr7:127297800-127311000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr7:127299000-127313400	Weak transcription	Gastric	stomach
22	chr7:127299000-127318600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr7:127299000-127334400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr7:127299400-127308600	Strong transcription	K562	blood
25	chr7:127299600-127315800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:127300600-127320400	Weak transcription	Placenta	Placenta
27	chr7:127300800-127319800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr7:127301600-127308600	Weak transcription	Dnd41	blood
29	chr7:127301600-127314000	Weak transcription	Fetal Lung	lung
30	chr7:127301800-127309200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr7:127301800-127315800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr7:127302000-127310200	Weak transcription	Fetal Muscle Leg	muscle
33	chr7:127302200-127309200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:127302800-127309200	Strong transcription	Primary T cells from cord blood	blood
35	chr7:127304400-127308800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr7:127304600-127309000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr7:127304600-127309400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:127304600-127314400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr7:127304600-127316200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr7:127304600-127326600	Weak transcription	Fetal Stomach	stomach
41	chr7:127304800-127319000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr7:127304800-127319000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr7:127305200-127310600	Weak transcription	Fetal Thymus	thymus
44	chr7:127305200-127311400	Weak transcription	Primary B cells from cord blood	blood
45	chr7:127305200-127313400	Weak transcription	Psoas Muscle	Psoas
46	chr7:127305200-127326600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr7:127305600-127308800	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr7:127305600-127309200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr7:127305800-127308600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr7:127305800-127308600	Enhancers	NH-A	brain

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