Variant report

Variant	rs12722976
Chromosome Location	chr1:103345744-103345745
allele	C/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	TCF12	chr1:103344937-103345772	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr1:103344900-103345808	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr1:103344875-103345818	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr1:103344849-103345778	SK-N-SH	brain:	n/a	n/a
5	JUND	chr1:103344936-103345759	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
COL11A1	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1020918	0.82[ASN][1000 genomes]
rs10874661	0.82[ASN][1000 genomes]
rs10874662	0.96[ASN][1000 genomes]
rs11164628	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11164629	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11164630	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11164632	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11164633	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12023984	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12133652	0.84[ASN][1000 genomes]
rs1241205	0.84[ASN][1000 genomes]
rs1241207	0.86[ASN][1000 genomes]
rs1241208	0.86[ASN][1000 genomes]
rs1271798	0.86[ASN][1000 genomes]
rs1318755	0.85[ASN][1000 genomes]
rs1318756	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1463048	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1676507	0.82[ASN][1000 genomes]
rs1676508	0.82[ASN][1000 genomes]
rs1763342	0.84[ASN][1000 genomes]
rs1763343	0.81[ASN][1000 genomes]
rs1763349	0.82[ASN][1000 genomes]
rs1841841	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1932331	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1932350	0.84[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2061705	0.84[CEU][hapmap]
rs2077569	0.97[ASN][1000 genomes]
rs2169608	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2169609	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2169610	0.86[ASN][1000 genomes]
rs2229783	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2616003	0.81[ASN][1000 genomes]
rs2783566	0.82[ASN][1000 genomes]
rs3753841	0.85[CHB][hapmap];1.00[YRI][hapmap]
rs4907985	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677574	0.82[ASN][1000 genomes]
rs945326	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs969272	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830882	chr1:103192683-103355802	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv522922	chr1:103305021-103764640	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv546928	chr1:103331349-103371652	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
4	nsv871829	chr1:103336601-103367095	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
5	nsv870600	chr1:103336601-103548497	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv871808	chr1:103339272-103367095	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
7	nsv870725	chr1:103339272-103371032	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
8	nsv870821	chr1:103339272-103379918	Active TSS ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv871809	chr1:103339272-103459537	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv871732	chr1:103339272-103466917	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv871475	chr1:103339272-103548497	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv546929	chr1:103342392-103371652	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
13	nsv462728	chr1:103342392-103455217	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv546930	chr1:103342392-103455217	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103334000-103349800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:103335400-103350000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:103338400-103369400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:103338800-103357200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:103339200-103349800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:103340800-103350000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:103341400-103349800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:103341600-103352000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:103342400-103349800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:103342800-103346000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:103343000-103345800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:103343400-103352000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:103343400-103355800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:103343400-103356200	Weak transcription	Fetal Heart	heart
15	chr1:103343400-103366000	Weak transcription	Fetal Brain Female	brain
16	chr1:103344400-103349800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:103345000-103345800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:103345000-103345800	Enhancers	NHDF-Ad	bronchial
19	chr1:103345000-103346000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:103345000-103346000	Enhancers	HSMM	muscle
21	chr1:103345000-103346000	Enhancers	NHLF	lung
22	chr1:103345000-103346400	Enhancers	HMEC	breast
23	chr1:103345000-103348000	Enhancers	HUVEC	blood vessel
24	chr1:103345200-103345800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:103345200-103345800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:103345200-103346200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:103345200-103346200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:103345400-103346200	Enhancers	NH-A	brain
29	chr1:103345400-103347000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:103345600-103346200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:103345600-103346400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:103345600-103346400	Enhancers	A549	lung
33	chr1:103345600-103346400	Enhancers	Osteobl	bone
34	chr1:103345600-103347200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:103345600-103347600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:103345600-103350600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:103345600-103385600	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links