Variant report

Variant	rs6696893
Chromosome Location	chr1:153479481-153479482
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153477007..153479814-chr1:153598279..153601276,3	MCF-7	breast:
2	chr1:153478376..153480788-chr1:153481314..153483652,2	K562	blood:
3	chr1:153478932..153480622-chr1:153722015..153724458,2	MCF-7	breast:
4	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
5	chr1:153479337..153482179-chr1:153578655..153582224,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163220	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000163218	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000243613	Chromatin interaction
ENSG00000189171	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs16835366	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16835368	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16835382	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16835393	0.86[ASN][1000 genomes]
rs17695220	0.89[ASN][1000 genomes]
rs1887039	0.86[ASN][1000 genomes]
rs1964151	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2339696	0.89[ASN][1000 genomes]
rs28410699	0.89[ASN][1000 genomes]
rs28464843	0.89[ASN][1000 genomes]
rs28632016	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28635377	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28676601	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28707433	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3915524	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845548	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845549	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845550	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845551	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845552	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845553	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845554	0.86[ASN][1000 genomes]
rs6587743	0.89[ASN][1000 genomes]
rs6587745	0.89[ASN][1000 genomes]
rs6587746	0.89[ASN][1000 genomes]
rs6660055	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6672390	0.84[EUR][1000 genomes]
rs6679509	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6690638	0.86[ASN][1000 genomes]
rs6690712	0.86[ASN][1000 genomes]
rs7515940	0.86[ASN][1000 genomes]
rs7520093	0.89[ASN][1000 genomes]
rs7534343	0.88[ASN][1000 genomes]
rs7534347	0.89[ASN][1000 genomes]
rs7534830	0.86[ASN][1000 genomes]
rs7537898	0.86[ASN][1000 genomes]
rs7544359	0.86[ASN][1000 genomes]
rs9436094	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9436095	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6696893	C1orf77	cis	intralobular white matter	BrainEAC

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153477800-153479600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:153477800-153480400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:153477800-153480800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:153477800-153480800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:153477800-153481000	Enhancers	Fetal Muscle Leg	muscle
6	chr1:153477800-153481200	Enhancers	Ovary	ovary
7	chr1:153478000-153479600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:153478000-153479600	Enhancers	NHDF-Ad	bronchial
9	chr1:153478000-153480200	Enhancers	Left Ventricle	heart
10	chr1:153478000-153480400	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr1:153478000-153481000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:153478000-153481000	Enhancers	Colon Smooth Muscle	Colon
13	chr1:153478000-153481000	Enhancers	HSMM	muscle
14	chr1:153478000-153481200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:153478000-153481200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:153478000-153482200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:153478000-153482600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:153478200-153479800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:153478400-153480600	Enhancers	Adipose Nuclei	Adipose
20	chr1:153478400-153480600	Enhancers	Fetal Lung	lung
21	chr1:153478400-153481000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:153478400-153481000	Enhancers	NHLF	lung
23	chr1:153478600-153480600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr1:153478800-153479800	Enhancers	Aorta	Aorta
25	chr1:153478800-153479800	Enhancers	Pancreas	Pancrea
26	chr1:153478800-153479800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr1:153478800-153480000	Enhancers	Right Ventricle	heart
28	chr1:153478800-153480200	Enhancers	Duodenum Mucosa	Duodenum
29	chr1:153478800-153480200	Enhancers	HSMMtube	muscle
30	chr1:153478800-153480400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr1:153478800-153480600	Enhancers	Placenta Amnion	Placenta Amnion
32	chr1:153478800-153480800	Enhancers	Fetal Intestine Large	intestine
33	chr1:153478800-153480800	Enhancers	Fetal Stomach	stomach
34	chr1:153478800-153481000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:153478800-153481000	Enhancers	Fetal Intestine Small	intestine
36	chr1:153478800-153481000	Enhancers	NH-A	brain
37	chr1:153478800-153481200	Enhancers	Fetal Muscle Trunk	muscle
38	chr1:153478800-153482200	Enhancers	NHEK	skin
39	chr1:153478800-153482400	Enhancers	HMEC	breast
40	chr1:153479000-153479800	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr1:153479000-153479800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:153479000-153479800	Enhancers	Liver	Liver
43	chr1:153479000-153479800	Enhancers	Placenta	Placenta
44	chr1:153479000-153479800	Enhancers	Gastric	stomach
45	chr1:153479000-153479800	Enhancers	Psoas Muscle	Psoas
46	chr1:153479000-153480000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:153479000-153480000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr1:153479000-153480000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:153479000-153480000	Enhancers	Esophagus	oesophagus
50	chr1:153479000-153480000	Enhancers	Right Atrium	heart

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