Variant report

Variant	rs10989168
Chromosome Location	chr9:103361114-103361115
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:103356597..103359532-chr9:103359671..103361180,2	K562	blood:
2	chr9:103360698..103363075-chr9:104159012..104161996,2	MCF-7	breast:
3	chr9:103279571..103281078-chr9:103358915..103361806,2	K562	blood:
4	chr9:103358110..103359783-chr9:103360702..103363224,2	MCF-7	breast:
5	chr9:103350659..103353280-chr9:103360412..103361939,2	K562	blood:
6	chr9:103278757..103281071-chr9:103359482..103361806,2	K562	blood:

Variant related genes	Relation type
ENSG00000136897	Chromatin interaction
ENSG00000136870	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1135455	0.95[ASN][1000 genomes]
rs1226588	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1226592	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1226594	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1226596	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13291670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13301089	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1760290	0.93[ASN][1000 genomes]
rs2151597	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2489363	0.94[ASN][1000 genomes]
rs2489364	0.93[ASN][1000 genomes]
rs2780958	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2780959	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2800288	0.97[ASN][1000 genomes]
rs72735191	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv893624	chr9:103351931-103416553	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10989168	RNF20	cis	parietal	SCAN
rs10989168	C9orf125	cis	cerebellum	SCAN
rs10989168	C9orf30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103359200-103361400	Enhancers	Fetal Heart	heart
2	chr9:103360200-103361800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:103360400-103361400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:103360600-103361200	Enhancers	Stomach Mucosa	stomach
5	chr9:103360600-103361400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr9:103360600-103361400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr9:103360600-103361400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:103360600-103361400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:103360600-103361400	Active TSS	Fetal Intestine Small	intestine
10	chr9:103360600-103361400	Active TSS	Gastric	stomach
11	chr9:103360600-103361600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr9:103360600-103361600	Active TSS	H9 Cell Line	embryonic stem cell
13	chr9:103360600-103361600	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr9:103360600-103361600	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr9:103360600-103361800	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr9:103360600-103361800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:103360600-103361800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr9:103360600-103361800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:103360600-103361800	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr9:103360600-103361800	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr9:103360600-103361800	Active TSS	A549	lung
22	chr9:103360600-103361800	Flanking Active TSS	HUVEC	blood vessel
23	chr9:103360600-103361800	Active TSS	Osteobl	bone
24	chr9:103360600-103362000	Active TSS	Rectal Smooth Muscle	rectum
25	chr9:103360800-103361200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:103360800-103361200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:103360800-103361200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
28	chr9:103360800-103361200	Active TSS	Primary T cells from cord blood	blood
29	chr9:103360800-103361200	Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr9:103360800-103361200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:103360800-103361200	Flanking Active TSS	Colonic Mucosa	Colon
32	chr9:103360800-103361200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
33	chr9:103360800-103361200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
34	chr9:103360800-103361200	Active TSS	Lung	lung
35	chr9:103360800-103361200	Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr9:103360800-103361400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr9:103360800-103361400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:103360800-103361400	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr9:103360800-103361400	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr9:103360800-103361400	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr9:103360800-103361400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:103360800-103361400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr9:103360800-103361400	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr9:103360800-103361400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr9:103360800-103361400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr9:103360800-103361400	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr9:103360800-103361400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr9:103360800-103361400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:103360800-103361400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr9:103360800-103361400	Active TSS	Primary T killer naive cells fromperipheralblood	blood

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