Variant report

Variant	rs952787
Chromosome Location	chr1:74972157-74972158
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:74971580..74976038-chr1:74977181..74980046,4	K562	blood:

Variant related genes	Relation type
ENSG00000162621	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12087130	1.00[GIH][hapmap]
rs12097159	0.93[ASN][1000 genomes]
rs3765673	0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs3765675	0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs3765678	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41289204	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522147	chr1:74338530-74983835	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1003171	chr1:74407468-75122270	Strong transcription Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv535000	chr1:74407468-75122270	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1007414	chr1:74726454-74976335	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv535002	chr1:74726454-74976335	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1010042	chr1:74798856-75001977	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1002903	chr1:74831209-74993866	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv830248	chr1:74962391-75144458	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs952787	CADM1	trans	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:74959800-74977800	Weak transcription	Left Ventricle	heart
2	chr1:74968600-74974200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:74969400-74972600	Enhancers	Fetal Heart	heart
4	chr1:74969600-74972200	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr1:74969600-74972400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:74969800-74973200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:74969800-74973400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:74970000-74973200	Enhancers	Fetal Brain Male	brain
9	chr1:74970400-74973000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:74970800-74972200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr1:74971000-74974200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:74971000-74974400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:74971000-74975600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:74971200-74972400	Enhancers	Fetal Brain Female	brain
15	chr1:74971200-74974600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:74971400-74972600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr1:74971600-74972200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:74971600-74972200	Enhancers	Brain Cingulate Gyrus	brain
19	chr1:74971600-74972400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr1:74971800-74972600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:74972000-74974400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links