Variant report

Variant	rs10778893
Chromosome Location	chr12:82754789-82754790
allele	A/G
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	NFYB	chr12:82754687-82755163	GM12878	blood:	n/a	chr12:82754881-82754896
2	SP1	chr12:82754726-82754988	GM12878	blood:	n/a	n/a
3	NFYB	chr12:82754673-82755151	K562	blood:	n/a	chr12:82754881-82754896
4	SP1	chr12:82754704-82755077	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:82742903..82744608-chr12:82753963..82756367,2	K562	blood:
2	chr12:82753358..82755104-chr12:82772991..82774509,2	K562	blood:
3	chr12:82750329..82753915-chr12:82754301..82756998,4	MCF-7	breast:

Variant related genes	Relation type
CCDC59	TF binding region
ENSG00000127720	Chromatin interaction
ENSG00000133773	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10778890	1.00[AFR][1000 genomes]
rs10778896	1.00[AFR][1000 genomes]
rs10778899	1.00[AFR][1000 genomes]
rs2717448	1.00[AFR][1000 genomes]
rs4509843	1.00[AFR][1000 genomes]
rs8181779	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559539	chr12:82280797-82896218	Genic enhancers Enhancers Strong transcription 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	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1041954	chr12:82314981-83008609	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv541550	chr12:82314981-83008609	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv832471	chr12:82578953-82755360	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv559541	chr12:82715210-83108395	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv899348	chr12:82744187-83169297	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:82753200-82754800	Weak transcription	Pancreas	Pancrea
2	chr12:82753200-82755400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:82753200-82755400	Weak transcription	Gastric	stomach
4	chr12:82753200-82755400	Weak transcription	Spleen	Spleen
5	chr12:82753200-82756000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:82753200-82767200	Weak transcription	Aorta	Aorta
7	chr12:82753200-82767800	Weak transcription	Esophagus	oesophagus
8	chr12:82753200-82767800	Weak transcription	Lung	lung
9	chr12:82753400-82755400	Weak transcription	Hela-S3	cervix
10	chr12:82753400-82755800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:82753400-82756800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr12:82753400-82756800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:82753400-82756800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:82753400-82761400	Weak transcription	Brain Anterior Caudate	brain
15	chr12:82753400-82763000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:82753400-82763200	Weak transcription	Placenta	Placenta
17	chr12:82753400-82763800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:82753400-82765200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:82753400-82765400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr12:82753400-82767400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:82753400-82767800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:82753400-82767800	Weak transcription	Thymus	Thymus
23	chr12:82753400-82768600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:82753400-82786200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:82753600-82755200	Weak transcription	Fetal Stomach	stomach
26	chr12:82753600-82755200	Weak transcription	Right Ventricle	heart
27	chr12:82753600-82756800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:82753600-82758000	Weak transcription	Left Ventricle	heart
29	chr12:82753600-82758000	Weak transcription	Psoas Muscle	Psoas
30	chr12:82753600-82758000	Weak transcription	HSMM	muscle
31	chr12:82753600-82763400	Weak transcription	Fetal Intestine Large	intestine
32	chr12:82753600-82763400	Weak transcription	Fetal Muscle Leg	muscle
33	chr12:82753600-82767600	Weak transcription	Primary B cells from cord blood	blood
34	chr12:82753600-82777800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:82753600-82782400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr12:82753600-82799800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:82753600-82805200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:82753800-82755600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr12:82753800-82756400	Weak transcription	A549	lung
40	chr12:82753800-82756800	Weak transcription	HSMMtube	muscle
41	chr12:82753800-82757000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:82753800-82758000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr12:82753800-82758000	Weak transcription	Right Atrium	heart
44	chr12:82753800-82759800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:82753800-82760000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr12:82753800-82761600	Weak transcription	Stomach Mucosa	stomach
47	chr12:82753800-82763000	Weak transcription	Primary T cells from cord blood	blood
48	chr12:82753800-82763200	Weak transcription	Fetal Intestine Small	intestine
49	chr12:82753800-82763400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr12:82753800-82767200	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links