Variant report

Variant	rs6448972
Chromosome Location	chr4:9709511-9709512
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	POLR2A	chr4:9709394-9709897	H1-hESC	embryonic stem cell:	n/a	n/a
2	TCF3	chr4:9709438-9710012	GM12878	blood:	n/a	chr4:9709801-9709815
3	PAX5	chr4:9709414-9710050	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:9704856-9709845	K562	blood:	n/a	n/a
5	TCF12	chr4:9709468-9709967	GM12878	blood:	n/a	chr4:9709597-9709604 chr4:9709805-9709812 chr4:9709599-9709606 chr4:9709804-9709814 chr4:9709598-9709608
6	POLR2A	chr4:9709507-9709982	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:9709483-9709980	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
ALG1L3P	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10002984	0.91[ASN][1000 genomes]
rs10010621	0.86[ASN][1000 genomes]
rs10014408	0.91[ASN][1000 genomes]
rs10805313	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10805314	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10939458	0.82[ASN][1000 genomes]
rs10939463	0.91[ASN][1000 genomes]
rs10939472	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10939473	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11730702	0.82[ASN][1000 genomes]
rs11944806	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13101652	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13101880	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13119702	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13136217	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2037315	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2867341	0.93[EUR][1000 genomes]
rs4260537	0.88[ASN][1000 genomes]
rs4407504	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4440216	0.91[ASN][1000 genomes]
rs4485817	0.90[ASN][1000 genomes]
rs4521347	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4532233	0.85[ASN][1000 genomes]
rs4554077	0.90[ASN][1000 genomes]
rs4554078	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4594723	0.94[ASN][1000 genomes]
rs4621430	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6448959	0.91[ASN][1000 genomes]
rs6448960	0.89[ASN][1000 genomes]
rs6812811	0.83[ASN][1000 genomes]
rs6829800	0.86[ASN][1000 genomes]
rs6844051	0.86[ASN][1000 genomes]
rs6851086	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6855355	0.85[ASN][1000 genomes]
rs6858093	0.89[ASN][1000 genomes]
rs7434744	0.87[ASN][1000 genomes]
rs7659176	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7664410	0.87[EUR][1000 genomes]
rs7678732	0.87[ASN][1000 genomes]
rs7680572	0.90[ASN][1000 genomes]
rs9291607	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9685755	0.84[ASN][1000 genomes]
rs9685887	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9761757	0.87[ASN][1000 genomes]
rs9995655	0.97[EUR][1000 genomes];0.82[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	esv1796218	chr4:9324644-9714338	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv428108	chr4:9324644-9764173	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv533218	chr4:9371016-10252290	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	74 gene(s)	inside rSNPs	diseases
4	nsv818213	chr4:9371116-9719981	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	esv2754610	chr4:9372303-9804524	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
6	nsv530090	chr4:9383695-10165033	Enhancers Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
7	nsv1012865	chr4:9429299-9794181	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1001143	chr4:9435322-9794181	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1011425	chr4:9436994-9715105	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1006867	chr4:9456977-9713612	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1002757	chr4:9456977-9715105	Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
12	nsv1012621	chr4:9456977-9802366	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
13	nsv1012634	chr4:9461218-9802366	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
14	nsv998043	chr4:9496282-9830208	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
15	esv10795	chr4:9508396-9745703	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
16	nsv878667	chr4:9543673-9903121	ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
17	nsv878669	chr4:9551094-9794724	Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
18	nsv469511	chr4:9609987-9754029	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
19	nsv482424	chr4:9609987-9754029	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv964031	chr4:9629449-9764955	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
21	nsv999102	chr4:9633247-9794181	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:9708600-9709800	Enhancers	Colonic Mucosa	Colon
2	chr4:9708600-9709800	Enhancers	Fetal Intestine Small	intestine
3	chr4:9708600-9709800	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr4:9708600-9709800	Enhancers	Stomach Mucosa	stomach
5	chr4:9708600-9710000	Enhancers	Spleen	Spleen
6	chr4:9708800-9709800	Enhancers	Gastric	stomach
7	chr4:9708800-9709800	Enhancers	Lung	lung
8	chr4:9709000-9709600	Weak transcription	Esophagus	oesophagus
9	chr4:9709000-9709600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr4:9709200-9709600	Active TSS	Duodenum Mucosa	Duodenum
11	chr4:9709200-9709600	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr4:9709400-9709800	Enhancers	Fetal Intestine Large	intestine

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