Variant report

Variant	rs6948730
Chromosome Location	chr7:3235579-3235580
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10229652	0.82[CEU][hapmap]
rs10269688	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10951116	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10951117	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2280651	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4719834	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4719836	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4722563	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs6972823	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026476	chr7:2965034-3311344	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv538656	chr7:2965034-3311344	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv464260	chr7:2966138-3315572	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv605874	chr7:2966138-3315572	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1018287	chr7:2967524-3298539	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv538657	chr7:2967524-3298539	Bivalent/Poised TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1015656	chr7:3131821-3321353	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1027009	chr7:3141609-3311344	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv538658	chr7:3141609-3311344	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv967449	chr7:3167678-3271703	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv464264	chr7:3194156-3349625	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv605880	chr7:3194156-3349625	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1032915	chr7:3195628-3251756	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv518337	chr7:3196333-3240101	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv525011	chr7:3196333-3264728	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv464265	chr7:3213851-3258801	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv605881	chr7:3213851-3258801	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv1023127	chr7:3216344-3466223	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
19	nsv464266	chr7:3218524-3258801	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv605882	chr7:3218524-3258801	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv518354	chr7:3220990-3286425	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6948730	INTS1	cis	cerebellum	SCAN
rs6948730	FOXK1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3231400-3237400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr7:3232000-3235600	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr7:3232000-3235800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:3232400-3235800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:3233400-3235600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:3233600-3235800	Enhancers	Pancreas	Pancrea
7	chr7:3234200-3235600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:3234200-3237400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr7:3234400-3235600	Enhancers	H1 Cell Line	embryonic stem cell
10	chr7:3234400-3235600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr7:3234400-3235600	Enhancers	NHLF	lung
12	chr7:3234800-3235600	Enhancers	NH-A	brain
13	chr7:3234800-3235800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr7:3234800-3236600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr7:3234800-3237800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr7:3234800-3240600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:3235000-3235600	Enhancers	HSMM	muscle
18	chr7:3235000-3235800	Enhancers	HepG2	liver
19	chr7:3235000-3236000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr7:3235000-3236400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr7:3235000-3236400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr7:3235000-3238000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr7:3235400-3236400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr7:3235400-3236800	Weak transcription	H9 Cell Line	embryonic stem cell

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