Variant report

Variant	rs10244632
Chromosome Location	chr7:50598703-50598704
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	MXI1	chr7:50598313-50601096	SK-N-SH	brain:	n/a	n/a
2	REST	chr7:50598616-50600621	H1-neurons	neurons:	n/a	n/a
3	EP300	chr7:50597088-50601096	SK-N-SH	brain:	n/a	chr7:50599946-50599960 chr7:50597383-50597399
4	POLR2A	chr7:50598571-50599332	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000226122	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10228056	0.86[JPT][hapmap]
rs10239937	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10249982	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10274275	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12535064	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12538830	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1451366	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1451368	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17133877	0.86[JPT][hapmap]
rs1817074	0.88[CHB][hapmap]
rs1901311	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1901312	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1982406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2100280	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2122818	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2122821	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2167366	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2198144	0.94[CHB][hapmap]
rs2329364	0.86[JPT][hapmap]
rs2876826	0.84[EUR][1000 genomes]
rs3735274	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4585697	0.93[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs4947584	0.93[CHB][hapmap]
rs4947588	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4947589	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56670620	0.89[ASN][1000 genomes]
rs58129743	0.89[ASN][1000 genomes]
rs6592961	0.87[CHB][hapmap]
rs6592963	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6592973	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67275148	0.89[ASN][1000 genomes]
rs6952023	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6963534	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6967361	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6970468	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6974583	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73121277	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7777600	0.84[EUR][1000 genomes]
rs7797142	0.81[EUR][1000 genomes]
rs7807564	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7808025	0.87[CHB][hapmap]
rs7809758	0.93[CHB][hapmap]
rs9918591	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9918702	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv888021	chr7:50538589-50610071	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr7:50589000-50599200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:50595200-50600000	Enhancers	Pancreas	Pancrea
4	chr7:50595200-50604600	Genic enhancers	Fetal Intestine Small	intestine
5	chr7:50595800-50599400	Enhancers	Fetal Intestine Large	intestine
6	chr7:50596200-50598800	Weak transcription	Brain Germinal Matrix	brain
7	chr7:50596200-50599000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:50596200-50599000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr7:50596200-50599200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:50596400-50599000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:50596800-50599000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:50597000-50598800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr7:50597000-50599000	Weak transcription	Gastric	stomach
14	chr7:50597000-50601200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:50597000-50601400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr7:50597200-50603600	Weak transcription	Liver	Liver
17	chr7:50597400-50598800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr7:50597400-50599000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:50597400-50599000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:50597400-50600000	Enhancers	Placenta	Placenta
21	chr7:50597400-50601400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr7:50597800-50601400	Weak transcription	HepG2	liver
23	chr7:50597800-50602400	Weak transcription	Stomach Mucosa	stomach
24	chr7:50598200-50598800	Enhancers	NHEK	skin
25	chr7:50598200-50599200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr7:50598200-50599400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr7:50598200-50600400	Enhancers	HMEC	breast
28	chr7:50598400-50600200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:50598600-50598800	Enhancers	A549	lung
30	chr7:50598600-50599000	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr7:50598600-50599000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr7:50598600-50599400	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr7:50598600-50600200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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