Variant report

Variant	rs7542900
Chromosome Location	chr1:95070041-95070042
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	chr1:95067748..95070486-chr1:95070993..95073979,4	K562	blood:
2	chr1:95068045..95070486-chr1:95071108..95072675,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10874865	0.84[EUR][1000 genomes]
rs1098724	0.97[ASN][1000 genomes]
rs1098726	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165173	0.90[JPT][hapmap]
rs11165176	0.84[EUR][1000 genomes]
rs12408608	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111860	0.83[EUR][1000 genomes]
rs1772895	0.99[ASN][1000 genomes]
rs2798940	0.97[ASN][1000 genomes]
rs34248730	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs841684	0.89[ASN][1000 genomes]
rs841685	0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs841687	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs841688	0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs841689	0.94[ASN][1000 genomes]
rs841690	0.93[ASN][1000 genomes]
rs841705	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs841708	0.97[ASN][1000 genomes]
rs866365	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870696	chr1:95005220-95081587	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv871391	chr1:95005220-95083836	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1001587	chr1:95027691-95318680	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv871279	chr1:95028981-95083836	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1804937	chr1:95051930-95081587	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Type 2 diabetes	22238593	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7542900	HFM1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95059400-95074200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:95061400-95076800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:95061600-95071600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:95062000-95072200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:95062400-95070800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:95065200-95081000	Enhancers	Stomach Mucosa	stomach
7	chr1:95065400-95081400	Enhancers	Fetal Intestine Small	intestine
8	chr1:95065600-95087200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:95066400-95070800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:95066400-95071400	Weak transcription	Pancreas	Pancrea
11	chr1:95066600-95071600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:95067600-95072000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:95068000-95071600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:95068000-95078200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:95068200-95070800	Weak transcription	Colonic Mucosa	Colon
16	chr1:95068200-95071400	Weak transcription	NHDF-Ad	bronchial
17	chr1:95068200-95073400	Weak transcription	Gastric	stomach
18	chr1:95068200-95074000	Enhancers	Duodenum Mucosa	Duodenum
19	chr1:95069000-95071600	Weak transcription	HepG2	liver
20	chr1:95069000-95072000	Weak transcription	HMEC	breast
21	chr1:95069200-95070400	Weak transcription	NH-A	brain
22	chr1:95069200-95071400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:95069200-95071600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:95069200-95071600	Weak transcription	Primary B cells from cord blood	blood
25	chr1:95069200-95074400	Weak transcription	NHLF	lung
26	chr1:95069400-95077800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:95069600-95070800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:95069600-95070800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:95069600-95071800	Weak transcription	Small Intestine	intestine
30	chr1:95069600-95072200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:95069600-95078200	Weak transcription	Dnd41	blood
32	chr1:95069800-95070200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:95070000-95070400	Weak transcription	Fetal Intestine Large	intestine
34	chr1:95070000-95071400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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