Variant report

Variant	rs13295838
Chromosome Location	chr9:843382-843383
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:843269..845393-chr9:851272..854140,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10739166	0.82[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap]
rs10815834	0.94[JPT][hapmap]
rs10815879	0.87[AMR][1000 genomes]
rs10815882	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10977097	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2181401	0.94[JPT][hapmap]
rs2273929	0.89[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2273930	0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs7020479	0.85[ASN][1000 genomes]
rs7025494	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7029148	0.82[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7865324	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7866179	0.81[ASN][1000 genomes]
rs7873478	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949051	chr9:40910-925305	Bivalent Enhancer Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1034557	chr9:209254-964422	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv539828	chr9:209254-964422	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv533964	chr9:314969-910448	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv931598	chr9:349034-862771	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1021206	chr9:399146-911325	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv916532	chr9:459131-862833	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv1025492	chr9:478813-1157169	Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv539897	chr9:478813-1157169	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	esv2758175	chr9:524413-853033	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
11	esv2759655	chr9:524413-853033	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
12	nsv427836	chr9:524413-853033	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
13	nsv1032909	chr9:546674-860810	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
14	nsv949533	chr9:584087-904106	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
15	nsv429977	chr9:584087-983301	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
16	nsv1034136	chr9:588657-964422	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
17	nsv1021740	chr9:596826-923709	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
18	nsv613037	chr9:643453-1138368	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
19	nsv1023836	chr9:646024-877740	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
20	nsv1017041	chr9:674129-860810	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
21	nsv892000	chr9:678951-972476	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
22	nsv1026138	chr9:685080-910449	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
23	nsv539907	chr9:685080-910449	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
24	nsv817248	chr9:706283-1457665	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
25	nsv1025998	chr9:790745-860810	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	nsv831491	chr9:794113-974142	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
27	nsv613047	chr9:802801-855091	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
28	nsv892003	chr9:822594-863635	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv892004	chr9:828348-863635	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	nsv892005	chr9:832711-853004	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	nsv892006	chr9:833828-863635	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
32	nsv892007	chr9:833828-883226	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
33	nsv892008	chr9:841152-883226	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
34	nsv892009	chr9:841152-947880	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
35	nsv892010	chr9:841152-1069663	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13295838	C9orf70	cis	cerebellum	SCAN
rs13295838	ENG	trans	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:841000-843400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
2	chr9:841200-843400	Bivalent Enhancer	Fetal Muscle Leg	muscle
3	chr9:841200-843400	Bivalent Enhancer	Placenta	Placenta
4	chr9:841400-843400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr9:841800-843400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr9:841800-843800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:842000-843400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:842400-843400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
9	chr9:842600-843400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:842600-843600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
11	chr9:842800-843400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:842800-843400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
13	chr9:842800-843400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr9:842800-843400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr9:842800-843400	Bivalent Enhancer	Fetal Intestine Large	intestine
16	chr9:842800-843400	Bivalent/Poised TSS	Right Ventricle	heart
17	chr9:842800-843600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
18	chr9:842800-843600	Bivalent/Poised TSS	Aorta	Aorta
19	chr9:843000-843400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:843000-843400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:843000-843400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:843000-843400	Bivalent Enhancer	Spleen	Spleen
23	chr9:843000-843600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
24	chr9:843200-843400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:843200-843400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
26	chr9:843200-843400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:843200-843400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
28	chr9:843200-843400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
29	chr9:843200-843600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
30	chr9:843200-843600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
31	chr9:843200-843800	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:843200-843800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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