Variant report

Variant	rs10797664
Chromosome Location	chr1:180988636-180988637
allele	C/T
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	chr1:180987607..180995372-chr1:181053215..181062450,34	MCF-7	breast:
2	chr1:180977340..180979634-chr1:180986263..180988829,3	K562	blood:
3	chr1:180523368..180525230-chr1:180988182..180990982,2	K562	blood:
4	chr1:180987703..180989736-chr1:180991727..180994304,2	K562	blood:
5	chr1:180611289..180612983-chr1:180987142..180989197,2	K562	blood:
6	chr1:180987722..180989814-chr1:181005943..181007789,2	MCF-7	breast:
7	chr1:180969304..180971404-chr1:180988525..180991376,2	K562	blood:
8	chr1:180969304..180970911-chr1:180988525..180990362,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000162783	Chromatin interaction
ENSG00000135823	Chromatin interaction
ENSG00000272198	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10753229	0.81[MKK][hapmap]
rs10910848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10910849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10910850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073184	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12411105	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068800	0.81[MKK][hapmap]
rs2331992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35672928	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4545301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652549	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692913	0.93[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	esv3342865	chr1:180933678-181018012	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3383831	chr1:180937224-181029755	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1011081	chr1:180973159-181135953	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10797664	ACBD6	cis	cerebellum	SCAN
rs10797664	NPL	cis	parietal	SCAN
rs10797664	STX6	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180959200-180990800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:180973800-180989600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:180973800-180990600	Weak transcription	Colonic Mucosa	Colon
4	chr1:180973800-180990800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:180974000-180990800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:180974400-180990000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:180974600-180990000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:180974600-180990600	Weak transcription	Liver	Liver
9	chr1:180974600-180990600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:180974600-180990600	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:180974800-180989800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:180974800-180990800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:180975000-180989600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:180975000-180990000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:180975200-180990200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:180980000-180991000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:180980400-180990600	Weak transcription	Fetal Stomach	stomach
18	chr1:180980600-180989600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:180980800-180989400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:180980800-180989600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:180980800-180989800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:180980800-180990000	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:180981000-180990200	Weak transcription	NH-A	brain
24	chr1:180981000-180990600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:180981200-180990400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:180981200-180991000	Weak transcription	Esophagus	oesophagus
27	chr1:180981400-180989600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:180981600-180989600	Weak transcription	Fetal Kidney	kidney
29	chr1:180981600-180989600	Weak transcription	Fetal Lung	lung
30	chr1:180981600-180989600	Weak transcription	HSMMtube	muscle
31	chr1:180981600-180990600	Weak transcription	Psoas Muscle	Psoas
32	chr1:180981600-180990600	Weak transcription	Right Atrium	heart
33	chr1:180981600-180990800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:180981800-180989600	Weak transcription	NHLF	lung
35	chr1:180982400-180989800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:180982800-180989600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:180982800-180991000	Weak transcription	Pancreas	Pancrea
38	chr1:180983000-180989400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:180983000-180990000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:180983000-180991200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:180984200-180990400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:180984200-180990600	Weak transcription	Aorta	Aorta
43	chr1:180984400-180990000	Weak transcription	Fetal Intestine Small	intestine
44	chr1:180984400-180990200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:180984400-180990800	Weak transcription	Ovary	ovary
46	chr1:180984400-180990800	Weak transcription	Small Intestine	intestine
47	chr1:180984600-180989800	Weak transcription	Thymus	Thymus
48	chr1:180984800-180990000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:180985000-180989800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:180985000-180991200	Weak transcription	Spleen	Spleen

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