Variant report

Variant	rs7044422
Chromosome Location	chr9:71352493-71352494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11143589	0.81[LWK][hapmap]
rs11789971	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12682815	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12686355	0.93[CHD][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.95[YRI][hapmap];0.81[ASN][1000 genomes]
rs13299226	0.81[ASN][1000 genomes]
rs34575286	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4745231	0.82[CHD][hapmap]
rs4745236	0.91[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7032100	0.90[LWK][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs7043892	0.95[YRI][hapmap]
rs7044032	0.95[YRI][hapmap];0.80[AFR][1000 genomes]
rs7044045	0.90[LWK][hapmap];0.95[YRI][hapmap]
rs953390	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026962	chr9:71130848-71357605	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh 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	15 gene(s)	inside rSNPs	diseases
3	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv2757339	chr9:71291107-71353743	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2759693	chr9:71291107-71353743	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv893415	chr9:71347988-71364351	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7044422	C9orf85	cis	parietal	SCAN
rs7044422	FAM189A2	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71342600-71354600	Enhancers	Fetal Intestine Large	intestine
2	chr9:71343400-71363000	Weak transcription	GM12878-XiMat	blood
3	chr9:71343800-71357200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr9:71344600-71354000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:71345600-71352800	Enhancers	Fetal Heart	heart
6	chr9:71346600-71353400	Weak transcription	Psoas Muscle	Psoas
7	chr9:71347200-71354600	Weak transcription	K562	blood
8	chr9:71347400-71357800	Weak transcription	Primary B cells from cord blood	blood
9	chr9:71348000-71354400	Weak transcription	Pancreas	Pancrea
10	chr9:71348200-71359000	Weak transcription	Lung	lung
11	chr9:71348400-71354600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:71349400-71353600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr9:71350000-71353400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:71350000-71353400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:71350000-71356600	Weak transcription	Aorta	Aorta
16	chr9:71350400-71354600	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr9:71350800-71353400	Weak transcription	HepG2	liver
18	chr9:71351000-71353400	Weak transcription	Right Atrium	heart
19	chr9:71351000-71353800	Weak transcription	Left Ventricle	heart
20	chr9:71351000-71354400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr9:71351000-71354600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr9:71351000-71354600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:71351000-71370600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr9:71351200-71352600	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr9:71351200-71353400	Weak transcription	Colonic Mucosa	Colon
26	chr9:71351200-71354600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:71351200-71354600	Weak transcription	Right Ventricle	heart
28	chr9:71351200-71355800	Enhancers	Fetal Intestine Small	intestine
29	chr9:71351200-71360000	Weak transcription	Gastric	stomach
30	chr9:71351600-71353600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:71351600-71353600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:71351800-71353000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr9:71352000-71353000	Weak transcription	Stomach Mucosa	stomach
34	chr9:71352200-71353400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr9:71352400-71353400	Weak transcription	Small Intestine	intestine
36	chr9:71352400-71365800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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