Variant report

Variant	rs9663790
Chromosome Location	chr10:49705636-49705637
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr10:49705233-49705745	SK-N-SH	brain:	n/a	chr10:49705448-49705460 chr10:49705450-49705459 chr10:49705450-49705457 chr10:49705449-49705459 chr10:49705449-49705459 chr10:49705449-49705458
2	ZNF384	chr10:49705503-49705703	K562	blood:	n/a	n/a
3	POLR2A	chr10:49704933-49706121	U87	brain:	n/a	n/a
4	POLR2A	chr10:49704900-49706127	U87	brain:	n/a	n/a
5	JUN	chr10:49705031-49706491	K562	blood:	n/a	chr10:49705448-49705460 chr10:49705450-49705459 chr10:49705450-49705457 chr10:49706340-49706348 chr10:49705449-49705459 chr10:49705449-49705459 chr10:49705449-49705458
6	JUND	chr10:49704930-49705902	SK-N-SH	brain:	n/a	chr10:49705448-49705460 chr10:49705450-49705459 chr10:49705450-49705457 chr10:49705449-49705459 chr10:49705449-49705459 chr10:49705449-49705458
7	JUND	chr10:49705251-49705655	K562	blood:	n/a	chr10:49705448-49705460 chr10:49705450-49705459 chr10:49705450-49705457 chr10:49705449-49705459 chr10:49705449-49705459 chr10:49705449-49705458
8	FOS	chr10:49705232-49705721	HUVEC	blood vessel:	n/a	chr10:49705448-49705460 chr10:49705450-49705459 chr10:49705450-49705457 chr10:49705448-49705459 chr10:49705449-49705459 chr10:49705449-49705459 chr10:49705449-49705458

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:49705591-49705641	T-47D	breast:	n/a
2	chr10:49705591-49705641	AG10803	skin:	n/a
3	chr10:49705591-49705641	GM19239	blood:	n/a
4	chr10:49705591-49705641	AoSMC	blood vessel:	n/a
5	chr10:49705591-49705641	HUVEC	blood vessel:	n/a
6	chr10:49705591-49705641	AG04449	skin:	fetal
7	chr10:49705591-49705641	NHBE	bronchial:	n/a
8	chr10:49705591-49705641	IMR90	lung:	fetal
9	chr10:49705591-49705641	HAEpiC	amniotic membrane:	n/a
10	chr10:49705591-49705641	GM12892	blood:	n/a
11	chr10:49705591-49705641	SAEC	small airway:	n/a
12	chr10:49705591-49705641	AG04450	lung:	fetal
13	chr10:49705591-49705641	A549	lung:	n/a
14	chr10:49705591-49705641	Hepatocyte	liver:	n/a
15	chr10:49705591-49705641	GM12878	blood:	n/a
16	chr10:49705591-49705641	NB4	blood:	n/a
17	chr10:49705591-49705641	Caco-2	colon:	n/a
18	chr10:49705591-49705641	HCM	heart:	n/a
19	chr10:49705591-49705641	HMEC	breast:	n/a
20	chr10:49705591-49705641	MCF-7	breast:	n/a
21	chr10:49705591-49705641	HEK293	kidney:	embryo
22	chr10:49705591-49705641	NT2-D1	testis:	n/a
23	chr10:49705591-49705641	HepG2	liver:	n/a
24	chr10:49705591-49705641	ovcar-3	ovarian:	n/a
25	chr10:49705591-49705641	H1-hESC	embryonic stem cell:	embryo
26	chr10:49705591-49705641	HL-60	blood:	n/a
27	chr10:49705591-49705641	NHDF-neo	bronchial:	n/a
28	chr10:49705591-49705641	PFSK-1	brain:	n/a
29	chr10:49705591-49705641	Jurkat	blood:	n/a
30	chr10:49705591-49705641	PANC-1	pancreas:	n/a
31	chr10:49705591-49705641	ECC-1	luminal epithelium:	n/a
32	chr10:49705591-49705641	ProgFib	skin:	n/a
33	chr10:49705591-49705641	HRE	kidney:	n/a
34	chr10:49705591-49705641	HRCEpiC	kidney:	n/a
35	chr10:49705591-49705641	GM12891	blood:	n/a
36	chr10:49705591-49705641	CMK	blood:	n/a
37	chr10:49705591-49705641	SKMC	muscle:	n/a
38	chr10:49705591-49705641	HCPEpiC	choroid plexus:	n/a
39	chr10:49705591-49705641	SK-N-SH	brain:	n/a
40	chr10:49705591-49705641	U87	brain:	n/a
41	chr10:49705591-49705641	HRPEpiC	eye:	n/a
42	chr10:49705591-49705641	HCT-116	colon:	n/a
43	chr10:49705591-49705641	AG09309	skin:	n/a
44	chr10:49705591-49705641	HCF	heart:	n/a
45	chr10:49705591-49705641	SK-N-SH_RA	brain:	n/a
46	chr10:49705591-49705641	K562	blood:	n/a
47	chr10:49705591-49705641	HPAEpiC	pulmonary alveolar:	n/a
48	chr10:49705591-49705641	SK-N-MC	brain:	n/a
49	chr10:49705591-49705641	NH-A	brain:	n/a
50	chr10:49705591-49705641	HIPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:49701131..49703834-chr10:49704395..49706982,4	K562	blood:
2	chr10:49700642..49703834-chr10:49704395..49707390,3	K562	blood:
3	chr10:49684937..49687761-chr10:49703928..49705850,2	MCF-7	breast:
4	chr10:49659900..49662821-chr10:49704182..49706648,2	K562	blood:
5	chr10:49698967..49701120-chr10:49704411..49706305,2	K562	blood:
6	chr10:49703894..49706471-chr10:49715514..49717897,2	K562	blood:

Variant related genes	Relation type
ARHGAP22	TF binding region
ARHGAP22	CpG island
ENSG00000128805	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10745277	0.89[ASN][1000 genomes]
rs10776607	0.90[ASN][1000 genomes]
rs10776608	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10776609	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10776610	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10857583	0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10857584	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10857585	0.91[ASN][1000 genomes]
rs10857586	0.82[ASN][1000 genomes]
rs10857590	0.82[JPT][hapmap]
rs11101343	0.91[ASN][1000 genomes]
rs11101370	0.89[CHD][hapmap];0.89[JPT][hapmap]
rs11101371	0.89[CHD][hapmap];0.89[JPT][hapmap]
rs12249815	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1814471	0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1867582	0.99[ASN][1000 genomes]
rs1947075	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs2377354	0.82[JPT][hapmap]
rs4838412	0.90[ASN][1000 genomes]
rs4838417	0.83[JPT][hapmap]
rs4838607	0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7913593	0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7913612	0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv467191	chr10:49669142-49735563	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv550813	chr10:49669142-49735563	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv550814	chr10:49705142-49735563	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9663790	TMEM72	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49698000-49731200	Weak transcription	Aorta	Aorta
2	chr10:49699200-49706000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr10:49699200-49706400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr10:49700600-49706800	Enhancers	K562	blood
5	chr10:49701400-49706000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr10:49701400-49706000	Enhancers	HMEC	breast
7	chr10:49701600-49716400	Weak transcription	Right Atrium	heart
8	chr10:49702200-49705800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr10:49702200-49707400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr10:49702400-49718200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr10:49703200-49706200	Genic enhancers	HSMM	muscle
12	chr10:49703200-49707000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr10:49703400-49706000	Enhancers	Placenta	Placenta
14	chr10:49703800-49705800	Enhancers	NHEK	skin
15	chr10:49703800-49706200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr10:49703800-49706200	Genic enhancers	Muscle Satellite Cultured Cells	--
17	chr10:49703800-49706400	Enhancers	HSMMtube	muscle
18	chr10:49704000-49706200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr10:49704200-49706000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr10:49704200-49706000	Enhancers	NH-A	brain
21	chr10:49704200-49706000	Enhancers	NHLF	lung
22	chr10:49704200-49707200	Enhancers	NHDF-Ad	bronchial
23	chr10:49704400-49706200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr10:49704400-49707800	Enhancers	Primary hematopoietic stem cells	blood
25	chr10:49704600-49705800	Enhancers	Placenta Amnion	Placenta Amnion
26	chr10:49704600-49706000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr10:49704600-49706000	Enhancers	Fetal Stomach	stomach
28	chr10:49704600-49706200	Enhancers	Fetal Thymus	thymus
29	chr10:49704600-49706600	Enhancers	Ovary	ovary
30	chr10:49704800-49705800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr10:49704800-49705800	Enhancers	Fetal Muscle Trunk	muscle
32	chr10:49704800-49706000	Enhancers	Fetal Muscle Leg	muscle
33	chr10:49704800-49706200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr10:49704800-49706200	Enhancers	HUVEC	blood vessel
35	chr10:49704800-49706200	Genic enhancers	Osteobl	bone
36	chr10:49705000-49705800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr10:49705000-49705800	Enhancers	Brain Hippocampus Middle	brain
38	chr10:49705000-49706000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr10:49705000-49706200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr10:49705000-49707200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr10:49705200-49705800	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr10:49705200-49706000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr10:49705200-49706000	Enhancers	Brain Anterior Caudate	brain
44	chr10:49705200-49706000	Enhancers	Stomach Smooth Muscle	stomach
45	chr10:49705200-49706000	Enhancers	Spleen	Spleen
46	chr10:49705400-49705800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr10:49705400-49716600	Weak transcription	Brain Angular Gyrus	brain
48	chr10:49705600-49706800	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr10:49705600-49708400	Weak transcription	Esophagus	oesophagus
50	chr10:49705600-49715600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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