Variant report

Variant	rs6746630
Chromosome Location	chr2:10280694-10280695
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	chr2:10278421-10282354	U87	brain:	n/a	n/a
2	POLR2A	chr2:10280349-10280725	K562	blood:	n/a	n/a
3	POLR2A	chr2:10280493-10280777	K562	blood:	n/a	n/a
4	SMC3	chr2:10280620-10283007	SK-N-SH	brain:	n/a	chr2:10280996-10281010 chr2:10282568-10282582 chr2:10280996-10281003 chr2:10281634-10281648
5	POLR2A	chr2:10271895-10281381	U87	brain:	n/a	n/a
6	POLR2A	chr2:10280653-10280772	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr2:10280502-10281077	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:10280507-10281875	K562	blood:	n/a	n/a
9	POLR2A	chr2:10280454-10280835	K562	blood:	n/a	n/a
10	POLR2A	chr2:10280424-10281221	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10278603..10281199-chr2:10574177..10576676,2	K562	blood:

Variant related genes	Relation type
C2orf48	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs62129879	0.81[AFR][1000 genomes]
rs62129883	0.81[EUR][1000 genomes]
rs73167390	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv873634	chr2:10275814-10337034	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10263800-10283600	Weak transcription	Spleen	Spleen
2	chr2:10264200-10281800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:10265400-10284000	Weak transcription	Placenta	Placenta
4	chr2:10269600-10299400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:10269800-10285200	Weak transcription	Brain Germinal Matrix	brain
6	chr2:10271400-10303800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:10272200-10284000	Weak transcription	GM12878-XiMat	blood
8	chr2:10272600-10289800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:10273400-10285000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:10273600-10282400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:10273600-10283400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:10273800-10281600	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:10273800-10281800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:10273800-10282000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:10273800-10282600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:10273800-10282600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:10273800-10283200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:10273800-10283400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr2:10273800-10283400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:10273800-10289800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:10273800-10330400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:10274000-10282000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:10274000-10299200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:10275200-10284200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:10275400-10281000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:10275400-10281400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:10276400-10307400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:10276600-10281800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr2:10276600-10284200	Weak transcription	NHLF	lung
30	chr2:10276600-10301800	Weak transcription	Osteobl	bone
31	chr2:10276800-10281600	Weak transcription	Fetal Stomach	stomach
32	chr2:10277000-10282000	Weak transcription	Fetal Intestine Small	intestine
33	chr2:10277200-10283400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:10277600-10280800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:10277600-10281000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:10277600-10282800	Weak transcription	Fetal Intestine Large	intestine
37	chr2:10277600-10283400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:10277600-10284000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:10277600-10321600	Weak transcription	K562	blood
40	chr2:10277800-10281000	Weak transcription	A549	lung
41	chr2:10277800-10281800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:10277800-10282000	Weak transcription	HepG2	liver
43	chr2:10277800-10295400	Weak transcription	Hela-S3	cervix
44	chr2:10278000-10281600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:10278000-10282000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:10278000-10282400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:10278000-10283400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:10278000-10302200	Weak transcription	HSMM	muscle
49	chr2:10278000-10311800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:10278200-10281000	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links