Variant report

Variant	rs6721644
Chromosome Location	chr2:10080554-10080555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10079779..10081937-chr2:10082992..10085179,2	MCF-7	breast:
2	chr2:10075342..10078182-chr2:10080340..10082783,2	K562	blood:

Variant related genes	Relation type
ENSG00000269973	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10803709	0.82[JPT][hapmap]
rs10929624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12468764	0.82[JPT][hapmap]
rs16867193	0.82[MEX][hapmap]
rs16867245	0.82[MEX][hapmap]
rs2052946	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288641	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288642	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357391	0.82[JPT][hapmap]
rs34577787	0.82[JPT][hapmap]
rs4668654	0.82[JPT][hapmap]
rs4669497	0.82[JPT][hapmap]
rs750872	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6721644	TAF1B	cis	cerebellum	SCAN
rs6721644	SERPINB4	trans	parietal	SCAN
rs6721644	NTSR2	cis	parietal	SCAN
rs6721644	TAF1B	cis	parietal	SCAN
rs6721644	GRHL1	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10030600-10080600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:10038600-10081400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:10049400-10081000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:10049600-10081200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:10055000-10080800	Weak transcription	Pancreas	Pancrea
6	chr2:10055000-10080800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:10055000-10081800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:10055200-10080800	Weak transcription	HMEC	breast
9	chr2:10059000-10080600	Weak transcription	HSMMtube	muscle
10	chr2:10059400-10081200	Weak transcription	GM12878-XiMat	blood
11	chr2:10061000-10080800	Weak transcription	Brain Germinal Matrix	brain
12	chr2:10061000-10080800	Weak transcription	NH-A	brain
13	chr2:10061000-10080800	Weak transcription	NHEK	skin
14	chr2:10063000-10080800	Weak transcription	NHLF	lung
15	chr2:10065000-10080800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:10070800-10080800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:10073400-10081800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:10073400-10084400	Weak transcription	Lung	lung
19	chr2:10073600-10088800	Weak transcription	Spleen	Spleen
20	chr2:10073800-10080800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:10073800-10080800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:10073800-10081000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:10073800-10082000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:10074000-10081800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:10074200-10081800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:10074400-10080800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:10075600-10080800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:10075600-10080800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:10075600-10080800	Weak transcription	NHDF-Ad	bronchial
30	chr2:10075600-10082400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:10075800-10080600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:10075800-10081200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:10075800-10081600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:10075800-10081600	Weak transcription	Placenta	Placenta
35	chr2:10076000-10081400	Weak transcription	Fetal Thymus	thymus
36	chr2:10076000-10081600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:10077000-10080800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:10078200-10081400	Weak transcription	A549	lung
39	chr2:10079200-10082400	Enhancers	Fetal Lung	lung
40	chr2:10079600-10080600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:10079600-10080600	Enhancers	HepG2	liver
42	chr2:10079600-10081000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:10079600-10081000	Enhancers	Fetal Intestine Large	intestine
44	chr2:10079600-10081200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:10079600-10082200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:10079800-10081000	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr2:10079800-10081600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:10079800-10082000	Enhancers	Stomach Mucosa	stomach
49	chr2:10079800-10082600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:10079800-10082600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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