Variant report

Variant	rs6699641
Chromosome Location	chr1:220162936-220162937
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:220161313-220168073	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:220153591..220159773-chr1:220159981..220165102,9	K562	blood:
2	chr1:220161264..220163445-chr1:220234115..220237098,2	K562	blood:
3	chr1:220072242..220074837-chr1:220162775..220165302,2	K562	blood:
4	chr1:220011035..220013766-chr1:220162762..220165197,2	K562	blood:

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

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10495143	0.99[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10779393	0.99[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10863523	0.99[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12046562	0.84[ASN][1000 genomes]
rs12048112	0.84[ASN][1000 genomes]
rs12058150	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291836	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291838	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3767669	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820457	0.81[ASN][1000 genomes]
rs61421597	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61830401	0.81[ASN][1000 genomes]
rs6669906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No data

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	chr1:220140600-220163000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:220140800-220163200	Strong transcription	Primary T cells from cord blood	blood
5	chr1:220140800-220164000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:220140800-220173400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:220140800-220192400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:220141000-220163000	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:220141000-220163200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:220141000-220163400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:220141200-220163200	Strong transcription	HSMM	muscle
12	chr1:220141200-220192200	Weak transcription	Fetal Kidney	kidney
13	chr1:220141400-220163400	Strong transcription	Dnd41	blood
14	chr1:220141400-220165400	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:220142200-220164000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:220142600-220169400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:220146400-220182800	Weak transcription	Spleen	Spleen
18	chr1:220147200-220169400	Weak transcription	Fetal Heart	heart
19	chr1:220147800-220163400	Strong transcription	K562	blood
20	chr1:220149000-220167400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:220149200-220163400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:220149400-220178200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:220149600-220166800	Weak transcription	Stomach Mucosa	stomach
24	chr1:220153600-220169200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:220154200-220169200	Weak transcription	Fetal Brain Male	brain
26	chr1:220154400-220169200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:220154400-220169200	Weak transcription	Fetal Lung	lung
28	chr1:220154600-220166200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:220154600-220167000	Weak transcription	Aorta	Aorta
30	chr1:220154600-220169000	Weak transcription	Small Intestine	intestine
31	chr1:220154600-220169200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:220154800-220167400	Weak transcription	Pancreas	Pancrea
33	chr1:220155000-220166000	Weak transcription	Brain Germinal Matrix	brain
34	chr1:220155600-220168600	Weak transcription	Brain Substantia Nigra	brain
35	chr1:220156000-220163400	Strong transcription	NHEK	skin
36	chr1:220156800-220164600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:220156800-220169800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:220157000-220168800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:220157200-220167000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:220157200-220177200	Weak transcription	Esophagus	oesophagus
41	chr1:220158200-220166000	Weak transcription	Lung	lung
42	chr1:220158200-220167200	Weak transcription	Ovary	ovary
43	chr1:220158200-220177200	Weak transcription	Right Ventricle	heart
44	chr1:220158400-220164800	Weak transcription	Fetal Intestine Small	intestine
45	chr1:220159000-220163200	Strong transcription	NH-A	brain
46	chr1:220159200-220163400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:220159200-220166200	Weak transcription	Fetal Stomach	stomach
48	chr1:220159200-220168800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:220159400-220163200	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:220159400-220163400	Strong transcription	Primary T helper cells fromperipheralblood	blood

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