Variant report

Variant	rs10992840
Chromosome Location	chr9:96428457-96428458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96212773..96214294-chr9:96426400..96428911,2	K562	blood:
2	chr9:96421764..96424036-chr9:96427270..96429397,3	K562	blood:

Variant related genes	Relation type
ENSG00000188938	Chromatin interaction
ENSG00000048828	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10122270	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs10761249	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10761250	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821185	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10821186	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10821187	0.92[EUR][1000 genomes]
rs10821188	0.92[EUR][1000 genomes]
rs10821189	0.92[EUR][1000 genomes]
rs10821190	0.96[EUR][1000 genomes]
rs10821191	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10821192	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821193	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821194	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821195	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821202	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10821203	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10992812	0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10992813	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10992815	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992819	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992829	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992831	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992842	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992860	0.88[CEU][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1132004	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1140722	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11534279	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs12238738	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1806524	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs2001315	0.91[EUR][1000 genomes]
rs2001589	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2001610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2398848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2398856	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs34031628	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34103739	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35171420	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36013568	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3750354	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs3750357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750359	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829758	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036592	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7040340	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7044244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7851178	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7851271	0.92[EUR][1000 genomes]
rs7864397	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7865712	1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs7868191	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs7871695	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1036609	chr9:96375217-96477641	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv893587	chr9:96383605-96451784	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv972421	chr9:96413056-96428661	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96400400-96430600	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr9:96401000-96430000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:96401000-96438600	Weak transcription	Psoas Muscle	Psoas
4	chr9:96402600-96430200	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:96402600-96433600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:96403400-96430800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:96403400-96430800	Strong transcription	Liver	Liver
8	chr9:96405200-96429200	Strong transcription	Duodenum Mucosa	Duodenum
9	chr9:96405200-96431400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr9:96405400-96430000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:96405400-96430600	Strong transcription	Primary T cells from cord blood	blood
12	chr9:96405400-96431400	Strong transcription	Fetal Brain Female	brain
13	chr9:96405400-96433200	Strong transcription	Fetal Intestine Small	intestine
14	chr9:96405600-96429800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr9:96405600-96430000	Strong transcription	Brain Germinal Matrix	brain
16	chr9:96405600-96430400	Strong transcription	Stomach Smooth Muscle	stomach
17	chr9:96406200-96438600	Weak transcription	Small Intestine	intestine
18	chr9:96406800-96430600	Strong transcription	Brain Hippocampus Middle	brain
19	chr9:96407200-96430400	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr9:96410000-96430200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr9:96410200-96428600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr9:96410400-96432600	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr9:96410400-96433200	Strong transcription	Gastric	stomach
24	chr9:96411800-96428600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr9:96412400-96430000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:96412600-96430000	Weak transcription	K562	blood
27	chr9:96412600-96439400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr9:96412600-96442800	Weak transcription	NHDF-Ad	bronchial
29	chr9:96412600-96445000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:96412800-96430600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:96412800-96442800	Weak transcription	HMEC	breast
32	chr9:96412800-96443600	Weak transcription	Stomach Mucosa	stomach
33	chr9:96413000-96432000	Strong transcription	Placenta	Placenta
34	chr9:96413000-96442000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr9:96413000-96444800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:96413200-96430800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr9:96413200-96440800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr9:96413400-96441600	Weak transcription	GM12878-XiMat	blood
39	chr9:96414200-96434800	Weak transcription	Right Atrium	heart
40	chr9:96414400-96435800	Weak transcription	HSMM	muscle
41	chr9:96416400-96443400	Weak transcription	HepG2	liver
42	chr9:96417800-96439000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr9:96419000-96431800	Weak transcription	Hela-S3	cervix
44	chr9:96419200-96440000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:96420800-96435600	Weak transcription	A549	lung
46	chr9:96422000-96439800	Weak transcription	Osteobl	bone
47	chr9:96424000-96430200	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr9:96424200-96429000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr9:96424200-96429800	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr9:96424200-96429800	Strong transcription	Dnd41	blood

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