Variant report

Variant	rs7537038
Chromosome Location	chr1:227470011-227470012
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227468377..227470578-chr1:227471178..227474571,3	K562	blood:
2	chr1:227453182..227454826-chr1:227468013..227470218,2	MCF-7	breast:
3	chr1:227468539..227470129-chr1:227473158..227475443,2	K562	blood:
4	chr1:227461391..227464005-chr1:227469962..227472348,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF678-5	chr1:227469373-227472002	l_204_chr1:227466302-227471954_brain

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10429872	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10495255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10737428	0.90[ASN][1000 genomes]
rs10753433	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799384	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs10799409	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10799410	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10916106	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10916108	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10916111	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916118	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916122	0.90[ASN][1000 genomes]
rs12035986	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12044287	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12065126	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12125514	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12137591	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12565056	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12565871	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12566059	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12569227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1304324	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs2102638	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2953638	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs2953652	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs2953655	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs3014252	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs3014253	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs3014256	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs3014267	0.82[JPT][hapmap]
rs34084723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34875093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35738984	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3795457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4339829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653797	0.84[AMR][1000 genomes]
rs4653812	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4653823	0.88[ASN][1000 genomes]
rs4653824	0.89[ASN][1000 genomes]
rs4653825	0.88[ASN][1000 genomes]
rs60197034	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6656653	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6682120	0.90[ASN][1000 genomes]
rs6684784	0.90[ASN][1000 genomes]
rs6684803	0.90[ASN][1000 genomes]
rs6685106	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6692294	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6697272	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6700730	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72759337	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7516326	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519752	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs955704	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3453491	chr1:227462942-227482283	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3453492	chr1:227462956-227482280	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
2	chr1:227443400-227474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:227447200-227473600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:227449600-227473600	Weak transcription	NH-A	brain
5	chr1:227454200-227470400	Weak transcription	Ovary	ovary
6	chr1:227458800-227472200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:227462600-227473600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:227462600-227500200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:227463000-227473000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:227464400-227472800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:227464400-227472800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:227465400-227472200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:227466200-227473200	Weak transcription	A549	lung
14	chr1:227466800-227472400	Weak transcription	Fetal Intestine Large	intestine
15	chr1:227467000-227472600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:227467200-227485800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:227468400-227471000	Weak transcription	Pancreas	Pancrea
18	chr1:227468600-227470200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
19	chr1:227468600-227472600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:227469000-227473000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:227469200-227473200	Weak transcription	HUVEC	blood vessel
22	chr1:227469200-227473600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:227469200-227477600	Weak transcription	Psoas Muscle	Psoas
24	chr1:227469200-227500200	Weak transcription	Left Ventricle	heart
25	chr1:227469200-227502600	Weak transcription	HSMM	muscle
26	chr1:227469400-227472200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:227469400-227472600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:227469400-227473200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:227469400-227477000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:227469600-227470400	Weak transcription	HMEC	breast
31	chr1:227469600-227471400	Weak transcription	Fetal Intestine Small	intestine
32	chr1:227469600-227472000	Weak transcription	Right Ventricle	heart
33	chr1:227469600-227472400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:227469600-227472400	Weak transcription	Right Atrium	heart
35	chr1:227469600-227473000	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:227469600-227473200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:227469600-227473400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:227469600-227473600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:227469600-227473600	Weak transcription	Aorta	Aorta
40	chr1:227469600-227501800	Weak transcription	Fetal Stomach	stomach
41	chr1:227470000-227470600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:227470000-227470600	ZNF genes & repeats	K562	blood

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