Variant report

Variant	rs4742710
Chromosome Location	chr9:100780515-100780516
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100779905..100783686-chr9:100794453..100797990,3	K562	blood:
2	chr9:100779685..100780554-chr9:100797234..100797778,2	K562	blood:
3	chr9:100774780..100779950-chr9:100780337..100785356,9	K562	blood:
4	chr9:100777690..100780620-chr9:100789410..100792089,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212521	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1010777	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10116946	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10125654	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10984606	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1131641	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572025	0.90[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1815275	0.91[ASN][1000 genomes]
rs4743152	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743154	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs56145417	0.94[EUR][1000 genomes]
rs7035650	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7044744	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7855077	0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7855088	0.90[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7870926	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7874518	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs879275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs987142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482635	chr9:100775549-100953239	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4742710	C9orf102	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100752000-100784000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:100754600-100784200	Strong transcription	Dnd41	blood
3	chr9:100754600-100784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:100755200-100782200	Strong transcription	HepG2	liver
5	chr9:100755200-100783800	Strong transcription	NHEK	skin
6	chr9:100755400-100783000	Weak transcription	Stomach Mucosa	stomach
7	chr9:100755600-100784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:100755800-100782200	Strong transcription	K562	blood
9	chr9:100756400-100783600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:100756400-100783800	Strong transcription	Fetal Muscle Trunk	muscle
11	chr9:100756400-100784400	Strong transcription	Fetal Thymus	thymus
12	chr9:100756600-100785600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr9:100756800-100781200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr9:100756800-100783000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:100756800-100783400	Strong transcription	HMEC	breast
16	chr9:100757000-100781000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr9:100757000-100785200	Strong transcription	Placenta	Placenta
18	chr9:100757200-100783600	Strong transcription	Liver	Liver
19	chr9:100757400-100784000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr9:100757600-100784400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr9:100757800-100782200	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:100758400-100780800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr9:100760800-100783600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr9:100761800-100784400	Strong transcription	Thymus	Thymus
25	chr9:100762600-100785400	Strong transcription	Primary T cells from cord blood	blood
26	chr9:100763800-100781800	Strong transcription	Hela-S3	cervix
27	chr9:100764400-100784200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr9:100764400-100784200	Strong transcription	GM12878-XiMat	blood
29	chr9:100765000-100781600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr9:100765600-100783000	Weak transcription	Right Atrium	heart
31	chr9:100765800-100782800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr9:100765800-100784000	Strong transcription	Adipose Nuclei	Adipose
33	chr9:100766000-100782400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr9:100766400-100783400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:100767000-100784600	Strong transcription	Fetal Stomach	stomach
36	chr9:100767200-100781400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr9:100767200-100782200	Strong transcription	Fetal Lung	lung
38	chr9:100767200-100782200	Strong transcription	Stomach Smooth Muscle	stomach
39	chr9:100767200-100782400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:100767200-100783200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:100767400-100781800	Strong transcription	Colon Smooth Muscle	Colon
42	chr9:100767800-100781000	Strong transcription	Rectal Smooth Muscle	rectum
43	chr9:100768200-100784000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr9:100770200-100784200	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr9:100770600-100788400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr9:100771600-100784600	Strong transcription	Brain Hippocampus Middle	brain
47	chr9:100772200-100784200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr9:100772400-100783600	Strong transcription	A549	lung
49	chr9:100772600-100781800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:100772600-100784200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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