Variant report

Variant	rs1694601
Chromosome Location	chr1:220163928-220163929
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:220163851-220163996	K562	blood:	n/a	n/a
2	POLR2A	chr1:220161313-220168073	K562	blood:	n/a	n/a
3	POLR2A	chr1:220163805-220164473	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:220153591..220159773-chr1:220159981..220165102,9	K562	blood:
2	chr1:220163102..220165191-chr1:220201695..220204471,2	K562	blood:
3	chr1:220144163..220148221-chr1:220163054..220166012,3	K562	blood:
4	chr1:220163484..220165362-chr1:220165481..220167153,2	K562	blood:
5	chr1:220163115..220165079-chr1:220292412..220294107,2	K562	blood:
6	chr1:220072242..220074837-chr1:220162775..220165302,2	K562	blood:
7	chr1:220011035..220013766-chr1:220162762..220165197,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238798	TF binding region
ENSG00000136628	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1061160	0.85[LWK][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs12140664	0.87[JPT][hapmap];0.85[YRI][hapmap]
rs1498393	0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs1624678	0.86[AFR][1000 genomes]
rs1694577	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1768666	0.87[JPT][hapmap];0.85[YRI][hapmap]
rs1768668	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1768672	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1768673	0.87[JPT][hapmap];0.85[YRI][hapmap]
rs2254494	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2454326	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2486328	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2647435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2647436	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2647437	0.86[AFR][1000 genomes]
rs2647459	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2647460	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2647463	0.85[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs2647468	0.81[AFR][1000 genomes]
rs2789795	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2789796	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767671	0.81[JPT][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	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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	744 gene(s)	inside rSNPs	diseases
2	nsv998124	chr1:220132739-220189211	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
3	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	738 gene(s)	inside rSNPs	diseases
4	esv1798515	chr1:220157811-220167371	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1694601	KCTD3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220132800-220177000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:220140000-220167400	Weak transcription	Gastric	stomach
3	chr1:220140800-220164000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:220140800-220173400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:220140800-220192400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:220141200-220192200	Weak transcription	Fetal Kidney	kidney
7	chr1:220141400-220165400	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:220142200-220164000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:220142600-220169400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:220146400-220182800	Weak transcription	Spleen	Spleen
11	chr1:220147200-220169400	Weak transcription	Fetal Heart	heart
12	chr1:220149000-220167400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:220149400-220178200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:220149600-220166800	Weak transcription	Stomach Mucosa	stomach
15	chr1:220153600-220169200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:220154200-220169200	Weak transcription	Fetal Brain Male	brain
17	chr1:220154400-220169200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:220154400-220169200	Weak transcription	Fetal Lung	lung
19	chr1:220154600-220166200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:220154600-220167000	Weak transcription	Aorta	Aorta
21	chr1:220154600-220169000	Weak transcription	Small Intestine	intestine
22	chr1:220154600-220169200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:220154800-220167400	Weak transcription	Pancreas	Pancrea
24	chr1:220155000-220166000	Weak transcription	Brain Germinal Matrix	brain
25	chr1:220155600-220168600	Weak transcription	Brain Substantia Nigra	brain
26	chr1:220156800-220164600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:220156800-220169800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:220157000-220168800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:220157200-220167000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:220157200-220177200	Weak transcription	Esophagus	oesophagus
31	chr1:220158200-220166000	Weak transcription	Lung	lung
32	chr1:220158200-220167200	Weak transcription	Ovary	ovary
33	chr1:220158200-220177200	Weak transcription	Right Ventricle	heart
34	chr1:220158400-220164800	Weak transcription	Fetal Intestine Small	intestine
35	chr1:220159200-220166200	Weak transcription	Fetal Stomach	stomach
36	chr1:220159200-220168800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:220159600-220164400	Strong transcription	NHDF-Ad	bronchial
38	chr1:220159800-220169200	Weak transcription	Colonic Mucosa	Colon
39	chr1:220160200-220168600	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:220160400-220167400	Weak transcription	Primary B cells from cord blood	blood
41	chr1:220160400-220168600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:220160600-220167000	Enhancers	Liver	Liver
43	chr1:220160800-220166000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:220160800-220169200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:220160800-220174200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:220161000-220164000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:220161000-220165400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:220161000-220167400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:220161000-220168800	Weak transcription	Colon Smooth Muscle	Colon
50	chr1:220161000-220168800	Weak transcription	Thymus	Thymus

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