Variant report

Variant	rs2398845
Chromosome Location	chr9:96365612-96365613
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96336608..96339307-chr9:96363926..96365665,2	K562	blood:
2	chr9:96363027..96365894-chr9:96366005..96367741,2	K562	blood:
3	chr9:96353562..96356481-chr9:96362305..96366209,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197724	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10117225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117691	0.90[JPT][hapmap]
rs10123378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10156602	0.95[CHB][hapmap]
rs10739951	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10761238	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs10761239	0.85[CHB][hapmap]
rs10761240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10761241	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10761242	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821160	0.81[CEU][hapmap]
rs10821164	0.85[CHB][hapmap]
rs10821166	0.85[CHB][hapmap]
rs10821168	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10821169	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821173	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821174	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821175	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821176	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821179	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821180	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10992792	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10992797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992798	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992799	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992800	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10992804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10992805	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11791934	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13291079	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs13294381	0.95[ASN][1000 genomes]
rs1412048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1412049	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2398846	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2398847	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895249	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4568663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7857266	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1040891	chr9:96361529-96397338	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1044461	chr9:96362048-96397338	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv893585	chr9:96363859-96403367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv893586	chr9:96363859-96493773	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96349000-96365800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:96352400-96366000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:96352400-96369200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:96352400-96384600	Weak transcription	NHLF	lung
5	chr9:96357000-96367000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:96361000-96369400	Weak transcription	Dnd41	blood
7	chr9:96361400-96372000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:96361400-96380400	Weak transcription	Fetal Brain Male	brain
9	chr9:96361600-96379400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:96363000-96366200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:96363000-96368600	Weak transcription	Fetal Lung	lung
12	chr9:96363200-96366000	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:96363200-96366000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:96363200-96366600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr9:96363200-96367400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:96363200-96367400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:96363200-96367600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:96363200-96367600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr9:96363200-96368000	Weak transcription	Adipose Nuclei	Adipose
20	chr9:96363200-96368800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr9:96363200-96369000	Weak transcription	Brain Anterior Caudate	brain
22	chr9:96363200-96374200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:96363200-96374600	Weak transcription	Gastric	stomach
24	chr9:96363200-96392000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr9:96363400-96366000	Weak transcription	Fetal Heart	heart
26	chr9:96363400-96366600	Strong transcription	Fetal Intestine Small	intestine
27	chr9:96363400-96367400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr9:96363400-96367600	Weak transcription	Primary B cells from cord blood	blood
29	chr9:96363400-96368600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:96363600-96367200	Weak transcription	Fetal Intestine Large	intestine
31	chr9:96363600-96367800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr9:96363600-96367800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr9:96363600-96383600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr9:96363800-96365800	Weak transcription	Colon Smooth Muscle	Colon
35	chr9:96363800-96366200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr9:96363800-96367600	Weak transcription	Primary T cells from cord blood	blood
37	chr9:96363800-96374000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr9:96363800-96374400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr9:96364000-96366000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr9:96364000-96366400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:96364000-96368800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr9:96364200-96365800	Weak transcription	Right Ventricle	heart
43	chr9:96364200-96366000	Strong transcription	Fetal Stomach	stomach
44	chr9:96364200-96366200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr9:96364200-96366200	Weak transcription	Fetal Muscle Leg	muscle
46	chr9:96364200-96369200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr9:96364200-96380600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr9:96364400-96366200	Weak transcription	Ovary	ovary
49	chr9:96365000-96366000	Weak transcription	Brain Germinal Matrix	brain
50	chr9:96365000-96366600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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