Variant report

Variant	rs9836231
Chromosome Location	chr3:136414321-136414322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10513014	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs1070232	0.93[JPT][hapmap]
rs10935186	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs11919030	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs12107125	0.81[ASN][1000 genomes]
rs12486911	1.00[YRI][hapmap]
rs12630999	0.93[JPT][hapmap]
rs12635723	0.93[JPT][hapmap]
rs1280624	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1681817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1729951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2062322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs35874192	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3856637	0.93[JPT][hapmap]
rs4038578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4038587	0.92[CEU][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4408829	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4521165	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4678433	0.93[JPT][hapmap]
rs4678437	0.93[JPT][hapmap]
rs4678438	0.93[JPT][hapmap]
rs6439649	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6439655	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6764567	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6789329	1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap]
rs6791142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6794351	0.93[JPT][hapmap]
rs6802702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6808312	0.93[JPT][hapmap]
rs699165	0.93[JPT][hapmap]
rs711975	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs7432375	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs7616204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7618518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7618871	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7621025	0.93[JPT][hapmap]
rs7634476	0.81[ASN][1000 genomes]
rs7637129	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs833752	0.93[JPT][hapmap]
rs900048	0.87[JPT][hapmap]
rs900818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs940174	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9813596	0.87[ASN][1000 genomes]
rs9825700	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9845762	0.93[JPT][hapmap]

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	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1008866	chr3:136364511-136427790	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9836231	DBR1	cis	cerebellum	SCAN
rs9836231	PCCB	cis	multi-tissue	Pritchard
rs9836231	PCCB	cis	parietal	SCAN
rs9836231	PCCB	cis	lymphoblastoid	seeQTL
rs9836231	SPSB4	cis	cerebellum	SCAN
rs9836231	PCCB	cis	cerebellum	SCAN
rs9836231	MSL2	cis	parietal	SCAN
rs9836231	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136390800-136447800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:136395000-136418200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:136408800-136414600	Weak transcription	Gastric	stomach
4	chr3:136409400-136417800	Weak transcription	Aorta	Aorta
5	chr3:136409400-136422000	Weak transcription	Lung	lung
6	chr3:136410600-136414800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:136411000-136415600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
8	chr3:136411000-136416200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:136411000-136444400	Weak transcription	Fetal Lung	lung
10	chr3:136411200-136415000	Weak transcription	NHDF-Ad	bronchial
11	chr3:136411400-136416800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:136411400-136417800	Weak transcription	Left Ventricle	heart
13	chr3:136411600-136416400	ZNF genes & repeats	Dnd41	blood
14	chr3:136411600-136419200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:136411600-136427800	Weak transcription	Right Ventricle	heart
16	chr3:136411800-136415000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:136411800-136415000	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:136411800-136416400	ZNF genes & repeats	Primary T cells from cord blood	blood
19	chr3:136411800-136417000	Weak transcription	Brain Substantia Nigra	brain
20	chr3:136412000-136415200	ZNF genes & repeats	Thymus	Thymus
21	chr3:136412000-136415400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
22	chr3:136412000-136415400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr3:136412000-136416200	ZNF genes & repeats	Primary B cells from cord blood	blood
24	chr3:136412400-136414400	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr3:136412600-136415000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:136412600-136416200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
27	chr3:136413200-136414400	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:136413200-136414600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:136413200-136415400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
30	chr3:136413200-136416000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:136413200-136420200	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:136413200-136420800	Weak transcription	Right Atrium	heart
33	chr3:136413400-136414400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:136413400-136414400	Weak transcription	Psoas Muscle	Psoas
35	chr3:136413400-136414800	Weak transcription	K562	blood
36	chr3:136413400-136415400	Weak transcription	Adipose Nuclei	Adipose
37	chr3:136413400-136423400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:136413400-136447200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:136413800-136414600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:136413800-136447800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:136414000-136415000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:136414000-136415400	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
43	chr3:136414200-136415200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
44	chr3:136414200-136415400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
45	chr3:136414200-136415400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:136414200-136415600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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