Variant report

Variant	rs2297596
Chromosome Location	chr9:97940968-97940969
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97933951..97937360-chr9:97938863..97941166,3	K562	blood:
2	chr9:97940064..97942185-chr9:97942262..97943911,2	MCF-7	breast:
3	chr9:97934712..97937360-chr9:97939666..97942024,2	K562	blood:

Variant related genes	Relation type
ENSG00000238746	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10115247	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1011784	0.91[JPT][hapmap]
rs10739992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739993	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10761374	0.86[JPT][hapmap]
rs10761377	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10761382	0.85[CEU][hapmap]
rs10821447	0.91[JPT][hapmap]
rs10821451	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10821453	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821454	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821455	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10993490	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13295862	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17686583	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2031599	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2166402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282216	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2297597	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404457	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3277	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34045846	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34532504	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3737142	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780561	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3780562	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3780564	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3780567	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3780568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3824486	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs3844341	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3852402	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4647382	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4647443	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4647459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4647462	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4647475	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4647528	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4647529	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4647534	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4647554	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4647558	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4657	0.91[JPT][hapmap]
rs4743988	0.91[JPT][hapmap]
rs4744442	0.91[JPT][hapmap]
rs4744446	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744451	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744454	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6479601	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7019043	0.85[EUR][1000 genomes]
rs7023007	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7027204	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7034538	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7042293	0.81[JPT][hapmap]
rs7042320	0.82[JPT][hapmap]
rs7046682	0.91[JPT][hapmap]
rs7850958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854570	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7872648	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7874310	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7874388	0.91[JPT][hapmap]
rs879492	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs881791	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs963774	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97906600-97950200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:97920000-97952000	Weak transcription	Aorta	Aorta
3	chr9:97920000-97952000	Weak transcription	Esophagus	oesophagus
4	chr9:97920400-97951800	Weak transcription	HepG2	liver
5	chr9:97925800-97944800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr9:97927600-97950400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr9:97930000-97945200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr9:97930000-97945400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:97930600-97943400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:97930600-97944800	Weak transcription	Lung	lung
11	chr9:97930600-97950400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr9:97930600-97950800	Weak transcription	Thymus	Thymus
13	chr9:97930600-97952000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:97930800-97941600	Weak transcription	Liver	Liver
15	chr9:97930800-97951600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr9:97930800-97952400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:97932200-97944800	Weak transcription	Primary T cells from cord blood	blood
18	chr9:97932200-97945000	Weak transcription	Fetal Intestine Large	intestine
19	chr9:97933200-97950600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr9:97933400-97945400	Weak transcription	Fetal Kidney	kidney
21	chr9:97933600-97944200	Weak transcription	Fetal Stomach	stomach
22	chr9:97937600-97941000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr9:97938200-97945200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:97938200-97945200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:97939600-97941400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr9:97939600-97950200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:97940000-97941000	Strong transcription	Fetal Intestine Small	intestine
28	chr9:97940000-97941000	Enhancers	Fetal Muscle Trunk	muscle
29	chr9:97940200-97950200	Weak transcription	Fetal Lung	lung
30	chr9:97940400-97941000	Enhancers	Fetal Thymus	thymus
31	chr9:97940600-97941000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:97940600-97941200	Enhancers	Gastric	stomach
33	chr9:97940600-97950600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr9:97940800-97941000	Genic enhancers	Pancreas	Pancrea
35	chr9:97940800-97950400	Weak transcription	Fetal Muscle Leg	muscle

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