Variant report

Variant	rs4707436
Chromosome Location	chr6:88851751-88851752
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10485171	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1049353	0.95[CEU][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59299454	0.90[EUR][1000 genomes]
rs7766029	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv604120	chr6:88818965-89198994	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1015298	chr6:88830630-89075508	Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv538355	chr6:88830630-89075508	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1020107	chr6:88838931-88866748	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2763586	chr6:88838943-88867488	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv519365	chr6:88842154-88861698	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv463944	chr6:88842154-88861698	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv463945	chr6:88842154-88861698	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv604121	chr6:88842154-88861698	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1023549	chr6:88842545-88869048	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4707436	RNGTT	cis	cerebellum	SCAN
rs4707436	SYNCRIP	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88843000-88853400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:88847600-88855800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:88848400-88855000	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:88850000-88855600	Enhancers	Primary B cells from peripheral blood	blood
5	chr6:88850400-88852400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:88850600-88859200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:88851000-88852000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:88851200-88852000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr6:88851200-88852000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr6:88851200-88852400	Flanking Active TSS	GM12878-XiMat	blood
11	chr6:88851400-88852000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr6:88851400-88852000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:88851400-88852000	Active TSS	Primary B cells from cord blood	blood
14	chr6:88851600-88851800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:88851600-88853000	Genic enhancers	Fetal Brain Female	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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