Variant report

Variant	rs9812791
Chromosome Location	chr3:49682311-49682312
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49673401..49676066-chr3:49680626..49682586,2	MCF-7	breast:
2	chr3:49682194..49684719-chr3:49702030..49703731,2	MCF-7	breast:
3	chr3:49594418..49597323-chr3:49680831..49683098,2	K562	blood:
4	chr3:49590854..49593809-chr3:49682054..49684437,3	K562	blood:

Variant related genes	Relation type
ENSG00000226913	Chromatin interaction
ENSG00000164061	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1050088	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs1060962	0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs10865955	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs11130199	0.86[JPT][hapmap]
rs11130212	0.97[ASN][1000 genomes]
rs11130213	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1131095	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11709525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710037	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711485	0.95[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap]
rs11718165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11720264	0.86[JPT][hapmap]
rs11720597	0.83[AMR][1000 genomes]
rs11917431	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11919311	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11921590	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12489092	0.86[JPT][hapmap]
rs13064576	0.86[AMR][1000 genomes]
rs13085791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13316695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352890	0.92[ASN][1000 genomes]
rs1568661	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs1801143	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap]
rs1873625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1873626	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2005557	0.81[ASN][1000 genomes]
rs2131104	0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs2131109	0.92[CHD][hapmap];0.88[GIH][hapmap]
rs2172252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329020	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2960548	0.87[ASN][1000 genomes]
rs3197999	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34762726	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];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35007338	0.92[ASN][1000 genomes]
rs35404120	0.92[ASN][1000 genomes]
rs35701831	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs3811697	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap]
rs3870338	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs3924462	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs4283605	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];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap]
rs4855839	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs4855847	0.92[ASN][1000 genomes]
rs4855852	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4855859	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs4855864	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs4855881	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4855884	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs6765869	0.81[ASN][1000 genomes]
rs6766131	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap]
rs6770670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803222	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7614725	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7622302	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs7633271	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs7637999	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs885592	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs9811982	1.00[CEU][hapmap]
rs9822268	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9823546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9824092	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827021	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9827708	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9833611	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9836291	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9837027	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap]
rs9837341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9837520	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9841110	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9853683	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs9858213	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs9858280	1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap]
rs9858542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862080	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875617	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs9882740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs9812791	MYL3	cis	parietal	SCAN
rs9812791	CELSR3	cis	cerebellum	SCAN
rs9812791	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs9812791	FAM212A	cis	Muscle Skeletal	GTEx
rs9812791	RBM6	cis	cerebellum	SCAN
rs9812791	RNF123	cis	cerebellum	SCAN
rs9812791	ZNF589	cis	parietal	SCAN
rs9812791	CISH	cis	lymphoblastoid	seeQTL
rs9812791	IP6K2	cis	cerebellum	SCAN
rs9812791	CCDC71	cis	cerebellum	SCAN
rs9812791	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9812791	GPX1	cis	parietal	SCAN
rs9812791	RNF123	cis	parietal	SCAN
rs9812791	PARP3	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49657600-49685400	Weak transcription	Brain Substantia Nigra	brain
2	chr3:49660800-49682600	Weak transcription	Liver	Liver
3	chr3:49661600-49692400	Weak transcription	Ovary	ovary
4	chr3:49662800-49685000	Weak transcription	Right Ventricle	heart
5	chr3:49664200-49683200	Weak transcription	Pancreas	Pancrea
6	chr3:49669400-49692000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:49673800-49692400	Weak transcription	Gastric	stomach
8	chr3:49675400-49688200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:49676000-49686400	Weak transcription	Spleen	Spleen
10	chr3:49676200-49692000	Weak transcription	Esophagus	oesophagus
11	chr3:49676400-49687000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:49679000-49682400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:49679400-49683000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:49679600-49687000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:49679800-49683000	Strong transcription	Fetal Brain Female	brain
16	chr3:49679800-49683200	Strong transcription	Brain Germinal Matrix	brain
17	chr3:49679800-49687600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr3:49680000-49682600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:49680000-49684800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:49680200-49682400	Strong transcription	Brain Anterior Caudate	brain
21	chr3:49680200-49684400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:49680400-49684800	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:49680600-49682600	Weak transcription	Psoas Muscle	Psoas
24	chr3:49681000-49682800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:49681000-49685400	Weak transcription	Fetal Stomach	stomach
26	chr3:49681200-49684800	Weak transcription	HepG2	liver
27	chr3:49681200-49688600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:49681200-49688800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:49681600-49683200	Weak transcription	Brain Angular Gyrus	brain
30	chr3:49681800-49682800	Enhancers	Placenta	Placenta
31	chr3:49682000-49682600	Enhancers	Adipose Nuclei	Adipose
32	chr3:49682000-49683200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:49682000-49684800	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr3:49682000-49685200	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:49682200-49689000	Weak transcription	Brain Cingulate Gyrus	brain

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