Variant report

Variant	rs943925
Chromosome Location	chr9:7175689-7175690
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1041288	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10758842	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10815534	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10976118	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10976119	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1467700	0.98[ASN][1000 genomes]
rs1887870	1.00[ASW][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1887872	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1928211	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2011128	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2014332	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2104682	0.95[ASN][1000 genomes]
rs2248904	0.93[ASN][1000 genomes]
rs2381571	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2381572	0.95[ASN][1000 genomes]
rs2494241	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2494242	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2770728	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2770729	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2770730	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2770733	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2770735	0.95[ASN][1000 genomes]
rs2770737	0.95[ASN][1000 genomes]
rs2770742	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2770745	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2770748	0.83[AMR][1000 genomes]
rs2770756	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2770760	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2820910	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2820918	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2820919	0.88[AMR][1000 genomes]
rs2820922	0.95[ASN][1000 genomes]
rs2820924	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2820925	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2820930	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2820934	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3753003	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs3829103	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7022345	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7029684	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7036627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs913591	0.93[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	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv613259	chr9:7032776-7541338	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1015874	chr9:7048807-7434890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer 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	3 gene(s)	inside rSNPs	diseases
5	nsv539971	chr9:7048807-7434890	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv892190	chr9:7094860-7186074	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv892192	chr9:7153009-7257340	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv528873	chr9:7163530-7177936	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
9	esv2758178	chr9:7175387-7482982	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv2759662	chr9:7175387-7482982	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs943925	C9orf68	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7148600-7185400	Weak transcription	HMEC	breast
2	chr9:7149600-7185400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:7149600-7186200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:7150400-7175800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:7151800-7188600	Weak transcription	Colonic Mucosa	Colon
6	chr9:7160800-7182000	Weak transcription	Dnd41	blood
7	chr9:7162600-7181600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr9:7162600-7182200	Weak transcription	Small Intestine	intestine
9	chr9:7163200-7177800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr9:7163400-7180600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr9:7163800-7179000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr9:7164000-7176200	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr9:7164600-7178000	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr9:7165800-7176200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr9:7165800-7179400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr9:7165800-7183800	Weak transcription	Esophagus	oesophagus
17	chr9:7165800-7185400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr9:7166200-7181000	Weak transcription	Hela-S3	cervix
19	chr9:7166400-7176800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:7167200-7185600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:7168200-7176400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:7169200-7183000	Strong transcription	Primary T cells from cord blood	blood
23	chr9:7169400-7176600	Strong transcription	Fetal Intestine Large	intestine
24	chr9:7169600-7176400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr9:7169600-7176600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr9:7169600-7176800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr9:7169800-7176600	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr9:7169800-7176600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr9:7169800-7176800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr9:7169800-7177600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr9:7170000-7176400	Strong transcription	Adipose Nuclei	Adipose
32	chr9:7170000-7176400	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr9:7170800-7176600	Enhancers	Placenta	Placenta
34	chr9:7171000-7176400	Strong transcription	Thymus	Thymus
35	chr9:7171200-7188200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:7171200-7193000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:7172000-7182400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr9:7172000-7183800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr9:7172200-7176600	Strong transcription	Fetal Intestine Small	intestine
40	chr9:7172600-7185400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr9:7172800-7176600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr9:7172800-7178600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr9:7172800-7185400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr9:7172800-7185400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr9:7172800-7185600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:7173000-7179000	Weak transcription	Brain Angular Gyrus	brain
47	chr9:7173000-7185600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr9:7173200-7176800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:7173200-7176800	Weak transcription	Fetal Brain Female	brain
50	chr9:7173200-7176800	Weak transcription	Fetal Kidney	kidney

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