Variant report

Variant	rs10759130
Chromosome Location	chr9:108471458-108471459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108459267..108461864-chr9:108470911..108472758,2	K562	blood:
2	chr9:108465735..108468384-chr9:108469174..108471784,2	K562	blood:
3	chr9:108469613..108472169-chr9:108477924..108480274,2	K562	blood:

Variant related genes	Relation type
ENSG00000095209	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10465120	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10816303	1.00[ASN][1000 genomes]
rs10816322	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10978195	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10978199	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10978201	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10978212	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978214	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978229	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11556047	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1567368	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17281274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3126472	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7025279	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7025786	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72730829	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849203	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893693	chr9:108427062-108683134	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv615116	chr9:108468129-108546438	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv968742	chr9:108471448-108472808	Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10759130	OR13C2	cis	parietal	SCAN
rs10759130	RNF20	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108457800-108472800	Weak transcription	Spleen	Spleen
2	chr9:108457800-108476200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:108457800-108492200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:108458000-108472400	Weak transcription	HSMM	muscle
5	chr9:108458000-108473000	Weak transcription	Left Ventricle	heart
6	chr9:108458000-108475200	Weak transcription	Fetal Thymus	thymus
7	chr9:108458000-108475600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:108458000-108475600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:108458000-108475600	Weak transcription	Thymus	Thymus
10	chr9:108458000-108476000	Weak transcription	Ovary	ovary
11	chr9:108458000-108479200	Weak transcription	Fetal Brain Male	brain
12	chr9:108458000-108497800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr9:108458200-108476400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:108458200-108478800	Weak transcription	Brain Hippocampus Middle	brain
15	chr9:108458200-108480800	Weak transcription	Brain Angular Gyrus	brain
16	chr9:108458200-108491400	Weak transcription	HSMMtube	muscle
17	chr9:108458200-108491600	Weak transcription	Brain Anterior Caudate	brain
18	chr9:108458200-108495400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:108458200-108497000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:108458600-108472600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr9:108459000-108476000	Weak transcription	Fetal Brain Female	brain
22	chr9:108459200-108472400	Weak transcription	Dnd41	blood
23	chr9:108459200-108489400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:108462600-108472600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr9:108463200-108478400	Weak transcription	Hela-S3	cervix
26	chr9:108463200-108496800	Weak transcription	HepG2	liver
27	chr9:108463400-108487600	Weak transcription	Primary B cells from cord blood	blood
28	chr9:108463800-108472400	Weak transcription	K562	blood
29	chr9:108464000-108474800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:108464200-108474800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr9:108464400-108471800	Weak transcription	Psoas Muscle	Psoas
32	chr9:108464400-108476000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr9:108465000-108496600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr9:108465600-108476200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:108466200-108476200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr9:108466800-108478400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr9:108467200-108473400	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr9:108467800-108472800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:108467800-108474200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:108468400-108475000	Weak transcription	Right Ventricle	heart
41	chr9:108468800-108475400	Weak transcription	Fetal Stomach	stomach
42	chr9:108469000-108476200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr9:108469000-108485000	Weak transcription	Small Intestine	intestine
44	chr9:108469200-108472800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr9:108469200-108475000	Weak transcription	Fetal Muscle Leg	muscle
46	chr9:108469200-108476000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr9:108469200-108478000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr9:108469400-108472400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr9:108469400-108473000	Weak transcription	Fetal Intestine Small	intestine
50	chr9:108469600-108472400	Weak transcription	Fetal Lung	lung

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