Variant report

Variant	rs12603708
Chromosome Location	chr17:16847113-16847114
allele	A/G
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	chr17:16846878-16847172	GM12891	blood:	n/a	n/a
2	STAT5A	chr17:16846680-16847324	GM12878	blood:	n/a	n/a
3	POLR2A	chr17:16845763-16848912	GM18505	blood:	n/a	n/a
4	POLR2A	chr17:16847064-16848246	GM18951	blood:	n/a	n/a
5	POLR2A	chr17:16845628-16849512	GM12892	blood:	n/a	n/a
6	POLR2A	chr17:16846099-16848820	GM12892	blood:	n/a	n/a
7	POLR2A	chr17:16846219-16849536	GM12892	blood:	n/a	n/a
8	NFATC1	chr17:16845899-16847187	GM12878	blood:	n/a	n/a
9	POLR2A	chr17:16846807-16847655	GM12878	blood:	n/a	n/a
10	POLR2A	chr17:16845221-16849358	GM12878	blood:	n/a	n/a
11	POLR2A	chr17:16845998-16849832	GM12892	blood:	n/a	n/a
12	POLR2A	chr17:16846057-16849577	GM12878	blood:	n/a	n/a
13	POLR2A	chr17:16846911-16848568	GM12878	blood:	n/a	n/a
14	POLR2A	chr17:16845599-16849822	GM12878	blood:	n/a	n/a
15	POLR2A	chr17:16846165-16849578	GM19193	blood:	n/a	n/a
16	POLR2A	chr17:16845984-16847242	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16825314..16827941-chr17:16845624..16848889,3	MCF-7	breast:
2	chr17:16844634..16847567-chr17:17108440..17110491,2	MCF-7	breast:

Variant related genes	Relation type
TNFRSF13B	TF binding region
ENSG00000179598	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11656532	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs2274892	0.86[CHB][hapmap];0.94[CHD][hapmap]
rs3818716	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs4383187	0.89[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4404112	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8078529	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv2753951	chr17:16660721-16848750	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2755100	chr17:16660721-16848750	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv833379	chr17:16683585-16859539	Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1055688	chr17:16800788-16868860	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv907726	chr17:16821204-16875636	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv275147	chr17:16845167-16848750	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12603708	SLC47A2	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16840800-16847400	Strong transcription	GM12878-XiMat	blood
2	chr17:16842600-16849200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:16843800-16848000	Enhancers	Fetal Muscle Leg	muscle
4	chr17:16844200-16848000	Weak transcription	Spleen	Spleen
5	chr17:16844200-16848600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr17:16844200-16848800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr17:16844200-16849000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr17:16844200-16849200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:16844200-16852000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr17:16844400-16848800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr17:16844400-16848800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr17:16844400-16848800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr17:16844800-16848600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr17:16844800-16848600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr17:16846200-16847800	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr17:16846400-16847600	Enhancers	Brain Substantia Nigra	brain
17	chr17:16846400-16848200	Enhancers	Brain Anterior Caudate	brain
18	chr17:16846400-16850400	Enhancers	Brain Hippocampus Middle	brain
19	chr17:16846400-16851600	Enhancers	Brain Cingulate Gyrus	brain
20	chr17:16846600-16847800	Weak transcription	Fetal Intestine Large	intestine
21	chr17:16846600-16848200	Weak transcription	Pancreas	Pancrea
22	chr17:16846600-16848800	Weak transcription	A549	lung
23	chr17:16846600-16849400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr17:16846600-16852000	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr17:16846800-16847400	Enhancers	Brain Angular Gyrus	brain
26	chr17:16847000-16847200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr17:16847000-16847200	Enhancers	Primary B cells from cord blood	blood

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