Variant report

Variant	rs10989170
Chromosome Location	chr9:103362510-103362511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:103360698..103363075-chr9:104159012..104161996,2	MCF-7	breast:
2	chr9:103358110..103359783-chr9:103360702..103363224,2	MCF-7	breast:
3	chr9:103361504..103363020-chr9:103366654..103368893,2	K562	blood:
4	chr9:103362495..103364857-chr9:103444927..103447653,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136870	Chromatin interaction
ENSG00000136897	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1000477	0.80[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs10465118	0.82[JPT][hapmap]
rs10465147	0.82[JPT][hapmap]
rs10465148	0.80[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs10465149	0.82[JPT][hapmap]
rs10512270	0.82[JPT][hapmap]
rs10512271	0.82[JPT][hapmap]
rs10819773	0.81[JPT][hapmap]
rs10819776	0.82[JPT][hapmap]
rs10819782	0.82[JPT][hapmap]
rs10819785	0.82[JPT][hapmap]
rs10819787	0.82[JPT][hapmap]
rs10819788	0.82[JPT][hapmap]
rs10819789	0.80[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs10819795	0.90[ASN][1000 genomes]
rs10989078	0.82[JPT][hapmap]
rs10989081	0.82[JPT][hapmap]
rs10989082	0.82[JPT][hapmap]
rs10989085	0.82[JPT][hapmap]
rs10989094	0.82[JPT][hapmap]
rs10989097	0.82[JPT][hapmap]
rs10989103	0.82[JPT][hapmap]
rs10989105	0.82[JPT][hapmap]
rs10989111	0.82[JPT][hapmap]
rs10989112	0.82[JPT][hapmap]
rs10989113	0.82[JPT][hapmap]
rs10989115	0.82[JPT][hapmap]
rs10989120	0.81[JPT][hapmap]
rs10989123	0.82[JPT][hapmap]
rs10989127	0.82[JPT][hapmap]
rs10989130	0.82[JPT][hapmap]
rs10989131	0.82[JPT][hapmap]
rs10989144	0.82[JPT][hapmap]
rs10989145	0.82[JPT][hapmap]
rs10989146	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs10989147	0.81[JPT][hapmap]
rs10989152	0.91[JPT][hapmap]
rs10989153	0.86[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs10989154	0.92[JPT][hapmap]
rs10989156	0.92[JPT][hapmap]
rs10989161	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10989162	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10989163	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10989164	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10989165	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10989167	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989169	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989173	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10989174	0.91[ASN][1000 genomes]
rs11793014	0.82[JPT][hapmap]
rs12004257	0.81[GIH][hapmap];0.82[JPT][hapmap]
rs12056981	0.82[JPT][hapmap]
rs12235981	0.92[JPT][hapmap]
rs12236071	0.82[JPT][hapmap]
rs12236970	0.81[GIH][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes]
rs12237481	0.82[JPT][hapmap]
rs12238560	0.82[JPT][hapmap]
rs12683122	0.82[JPT][hapmap]
rs12683548	0.82[JPT][hapmap]
rs12683889	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12684438	0.82[JPT][hapmap]
rs12684454	0.82[JPT][hapmap]
rs12685564	0.95[ASN][1000 genomes]
rs13295029	0.87[MEX][hapmap];0.89[TSI][hapmap]
rs1332598	0.82[JPT][hapmap]
rs16919174	0.82[JPT][hapmap]
rs16919204	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16919211	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1930246	0.80[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs1931140	0.92[JPT][hapmap];0.82[EUR][1000 genomes]
rs2026423	0.80[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs2069236	0.80[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs2151106	0.82[JPT][hapmap]
rs2183989	0.82[JPT][hapmap]
rs2183990	0.82[JPT][hapmap]
rs2183991	0.82[JPT][hapmap]
rs2274881	0.82[JPT][hapmap]
rs2274882	0.82[JPT][hapmap]
rs28623148	0.98[ASN][1000 genomes]
rs35919153	0.83[EUR][1000 genomes]
rs4454331	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55757829	0.96[ASN][1000 genomes]
rs56290508	0.96[ASN][1000 genomes]
rs56354846	0.96[ASN][1000 genomes]
rs59823190	0.80[EUR][1000 genomes]
rs7021028	0.86[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7028822	0.80[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs7029001	0.82[JPT][hapmap]
rs7042669	0.82[JPT][hapmap]
rs7046659	0.82[JPT][hapmap]
rs72735197	0.87[ASN][1000 genomes]
rs7850353	0.83[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10989170	C9orf21	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103361200-103372800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:103361600-103362800	Weak transcription	HSMMtube	muscle
3	chr9:103361600-103363800	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr9:103361600-103364400	Enhancers	Fetal Muscle Leg	muscle
5	chr9:103361800-103362800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:103361800-103362800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:103361800-103362800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr9:103361800-103362800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr9:103361800-103362800	Weak transcription	HSMM	muscle
10	chr9:103361800-103363000	Weak transcription	Brain Hippocampus Middle	brain
11	chr9:103361800-103363000	Weak transcription	Psoas Muscle	Psoas
12	chr9:103361800-103363200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:103361800-103363200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:103361800-103363200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:103361800-103363600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr9:103361800-103363600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr9:103361800-103363600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:103361800-103363600	Enhancers	NHEK	skin
19	chr9:103361800-103363800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr9:103361800-103363800	Weak transcription	Lung	lung
21	chr9:103361800-103364600	Weak transcription	Fetal Brain Male	brain
22	chr9:103361800-103364600	Weak transcription	Right Atrium	heart
23	chr9:103361800-103364800	Weak transcription	Brain Anterior Caudate	brain
24	chr9:103361800-103364800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:103361800-103367600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:103362000-103362800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr9:103362000-103362800	Weak transcription	K562	blood
28	chr9:103362000-103363000	Weak transcription	HepG2	liver
29	chr9:103362000-103363600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr9:103362000-103363600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:103362000-103363800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr9:103362000-103364600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr9:103362200-103362600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:103362200-103362600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:103362200-103364600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links