Variant report

Variant	rs11961008
Chromosome Location	chr6:166943745-166943746
allele	A/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	USF1	chr6:166943727-166944061	A549	lung:	n/a	chr6:166943893-166943904
2	USF1	chr6:166943530-166944655	HCT-116	colon:	n/a	chr6:166943893-166943904
3	USF1	chr6:166943744-166943990	A549	lung:	n/a	chr6:166943893-166943904
4	MAX	chr6:166943700-166944608	MCF-7	breast:	n/a	chr6:166944338-166944347
5	USF1	chr6:166943492-166944393	HCT-116	colon:	n/a	chr6:166943893-166943904
6	MAX	chr6:166943592-166944659	HCT-116	colon:	n/a	chr6:166944338-166944347
7	POLR2A	chr6:166943744-166944126	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:166938386..166940136-chr6:166942749..166944700,2	K562	blood:

Variant related genes	Relation type
ENSG00000269048	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11961547	0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11962002	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11962046	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11962068	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11962104	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11962129	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11962190	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11962191	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11962250	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11962691	0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11962718	0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11964246	0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11964912	0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11967122	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11968040	0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11969346	0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11969535	0.83[CEU][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11969688	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11970138	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11970162	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11970189	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11970312	1.00[CEU][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17584003	0.82[EUR][1000 genomes]
rs33973677	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35007078	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3752548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3799644	1.00[CHB][hapmap]
rs3799648	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3799649	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3799650	0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3799651	0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3799653	0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3799663	0.82[EUR][1000 genomes]
rs6903487	1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6908724	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6908895	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6923077	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6923273	0.82[EUR][1000 genomes]
rs6924732	0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73788028	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][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	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886941	chr6:166907173-166996991	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv605259	chr6:166936021-166952981	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166901000-166954800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:166902200-166954400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:166902600-166952800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:166909600-166943800	Weak transcription	Colonic Mucosa	Colon
5	chr6:166913000-166952000	Weak transcription	Primary T cells from cord blood	blood
6	chr6:166916200-166954200	Weak transcription	Right Atrium	heart
7	chr6:166923000-166943800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:166923200-166943800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:166923800-166944400	Weak transcription	Psoas Muscle	Psoas
10	chr6:166923800-166953000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr6:166929600-166954000	Weak transcription	HSMM	muscle
12	chr6:166929600-166955600	Weak transcription	HMEC	breast
13	chr6:166930200-166944000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:166930400-166943800	Weak transcription	Esophagus	oesophagus
15	chr6:166930400-166954200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:166930400-166957800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:166932400-166948600	Weak transcription	Primary B cells from cord blood	blood
18	chr6:166932600-166953800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:166933200-166953200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr6:166933800-166953400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:166934400-166944000	Weak transcription	Fetal Intestine Large	intestine
22	chr6:166935400-166952000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:166935400-166966400	Weak transcription	NH-A	brain
24	chr6:166935600-166943800	Weak transcription	Fetal Intestine Small	intestine
25	chr6:166938000-166943800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:166938200-166948800	Weak transcription	HUVEC	blood vessel
27	chr6:166938200-166955800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:166939400-166943800	Weak transcription	Spleen	Spleen
29	chr6:166940000-166944800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:166940800-166943800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:166940800-166953000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:166941000-166945200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:166941000-166954600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:166941400-166954600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:166941400-166955600	Weak transcription	Colon Smooth Muscle	Colon
36	chr6:166941600-166943800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:166941600-166943800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr6:166941600-166944000	Weak transcription	Ovary	ovary
39	chr6:166941800-166943800	Weak transcription	NHLF	lung
40	chr6:166941800-166954800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr6:166942000-166947400	Weak transcription	Small Intestine	intestine
42	chr6:166942200-166944200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr6:166942400-166954200	Weak transcription	NHEK	skin
44	chr6:166942600-166944600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:166942600-166946400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:166942800-166943800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:166942800-166944000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:166942800-166944200	Strong transcription	Stomach Mucosa	stomach
49	chr6:166942800-166944400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:166942800-166944600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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