Variant report

Variant	rs12336790
Chromosome Location	chr9:101938599-101938600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101932774..101936313-chr9:101937210..101940829,5	K562	blood:
2	chr9:101937724..101939532-chr9:101941994..101944179,2	K562	blood:
3	chr9:101936506..101939431-chr9:101943507..101946990,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227269	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10114715	1.00[CEU][hapmap];0.87[JPT][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10121020	0.87[YRI][hapmap]
rs10819641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988740	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10988743	0.82[CEU][hapmap];0.89[CHB][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10988744	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10988745	1.00[CEU][hapmap];0.80[YRI][hapmap]
rs10988746	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes]
rs10988749	1.00[CEU][hapmap]
rs12336513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12340839	1.00[CEU][hapmap]
rs12340952	0.80[YRI][hapmap]
rs12345762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13440104	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs16918352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59091994	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6478976	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs7022989	0.82[JPT][hapmap];0.83[YRI][hapmap]
rs7872043	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs912248	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs912249	1.00[CEU][hapmap];0.87[EUR][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	nsv831666	chr9:101874985-102018690	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101931600-101947000	Weak transcription	Right Atrium	heart
2	chr9:101932200-101940200	Enhancers	Fetal Intestine Large	intestine
3	chr9:101935200-101939000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr9:101935200-101941000	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:101935200-101947200	Weak transcription	Gastric	stomach
6	chr9:101935800-101939200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:101936400-101941400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr9:101936400-101943800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:101936600-101938800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:101936600-101938800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:101936600-101949600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr9:101936800-101938800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:101936800-101939000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:101937000-101938800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:101937000-101938800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr9:101937000-101938800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr9:101937000-101938800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:101937600-101939800	Enhancers	HepG2	liver
19	chr9:101937800-101940200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:101937800-101940200	Enhancers	Fetal Intestine Small	intestine
21	chr9:101938400-101938800	Weak transcription	GM12878-XiMat	blood
22	chr9:101938400-101939800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:101938400-101939800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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