Variant report

Variant	rs12547077
Chromosome Location	chr8:6417834-6417835
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	chr8:6417306..6418909-chr8:6419114..6421148,2	K562	blood:
2	chr8:6407291..6408244-chr8:6417821..6418628,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091879	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11996740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12541109	0.90[ASN][1000 genomes]
rs12543837	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12545089	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12546072	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12546205	1.00[CHB][hapmap]
rs12547116	0.83[ASN][1000 genomes]
rs12549365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17077573	1.00[CHB][hapmap]
rs17553929	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs17553964	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17554274	1.00[CHB][hapmap]
rs17623747	0.90[CHB][hapmap]
rs17624022	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17624399	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17624865	1.00[CHB][hapmap]
rs2442528	0.81[CHB][hapmap]
rs2442551	1.00[CHB][hapmap]
rs2515514	1.00[CHB][hapmap]
rs2922826	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2922840	1.00[CHB][hapmap]
rs2922841	1.00[CHB][hapmap]
rs2922842	1.00[CHB][hapmap]
rs2922843	1.00[CHB][hapmap]
rs2922845	1.00[CHB][hapmap]
rs2959776	0.89[CHB][hapmap]
rs3739390	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3739392	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55993125	0.87[ASN][1000 genomes]
rs56076232	0.88[ASN][1000 genomes]
rs56112478	0.88[ASN][1000 genomes]
rs73661404	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7817104	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7820827	1.00[CHB][hapmap]
rs7832816	0.88[ASN][1000 genomes]
rs7833871	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7838154	1.00[CHB][hapmap]
rs921291	0.89[CEU][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890034	chr8:5926632-6427868	Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3506199	chr8:6116693-6536592	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	esv3506200	chr8:6116693-6536592	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv933282	chr8:6261036-6440592	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS 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	8 gene(s)	inside rSNPs	diseases
7	nsv1015981	chr8:6286575-6578450	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv890057	chr8:6317165-6427868	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1021684	chr8:6350091-6809455	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	esv2422383	chr8:6362389-6781593	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv610004	chr8:6402366-6772913	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv1029241	chr8:6411300-6761720	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12547077	MCPH1	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6342400-6421400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr8:6364200-6478200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr8:6373600-6420200	Weak transcription	Esophagus	oesophagus
4	chr8:6405800-6418400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr8:6405800-6419400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr8:6405800-6419400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr8:6407800-6423800	Weak transcription	Spleen	Spleen
8	chr8:6408800-6418400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr8:6408800-6419400	Weak transcription	Fetal Stomach	stomach
10	chr8:6410400-6419000	Weak transcription	Primary T cells from cord blood	blood
11	chr8:6411000-6419800	Weak transcription	Colonic Mucosa	Colon
12	chr8:6413600-6419400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr8:6415200-6424000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr8:6415400-6418000	Enhancers	Primary hematopoietic stem cells	blood
15	chr8:6415400-6419000	Enhancers	NHLF	lung
16	chr8:6415400-6419400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr8:6415600-6420200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr8:6415800-6418000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr8:6416000-6419600	Flanking Active TSS	HUVEC	blood vessel
20	chr8:6416400-6418400	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr8:6416400-6418400	Enhancers	Fetal Thymus	thymus
22	chr8:6416400-6418800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr8:6416400-6419400	Enhancers	Primary B cells from cord blood	blood
24	chr8:6416400-6420800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr8:6416400-6422200	Enhancers	Primary B cells from peripheral blood	blood
26	chr8:6416600-6418400	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr8:6416600-6418800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr8:6416600-6418800	Enhancers	Fetal Intestine Small	intestine
29	chr8:6416600-6418800	Enhancers	Stomach Mucosa	stomach
30	chr8:6416600-6419200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr8:6416600-6420800	Active TSS	Right Atrium	heart
32	chr8:6416600-6421000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr8:6416600-6421000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr8:6416800-6419400	Active TSS	Adipose Nuclei	Adipose
35	chr8:6416800-6419400	Weak transcription	Gastric	stomach
36	chr8:6416800-6419600	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr8:6416800-6420200	Active TSS	Psoas Muscle	Psoas
38	chr8:6416800-6420800	Active TSS	Right Ventricle	heart
39	chr8:6416800-6442400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr8:6417000-6418000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr8:6417000-6418000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr8:6417000-6418000	Enhancers	Liver	Liver
43	chr8:6417000-6418400	Active TSS	Lung	lung
44	chr8:6417000-6419400	Active TSS	Brain Germinal Matrix	brain
45	chr8:6417000-6419400	Active TSS	Placenta	Placenta
46	chr8:6417000-6419600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr8:6417000-6421200	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr8:6417200-6418000	Enhancers	Fetal Kidney	kidney
49	chr8:6417200-6418000	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr8:6417200-6418400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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