Variant report

Variant	rs1873625
Chromosome Location	chr3:49666964-49666965
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49664437..49667415-chr3:49710388..49712286,2	K562	blood:
2	chr3:49666595..49669232-chr3:49671512..49673692,2	K562	blood:
3	chr3:49666488..49668184-chr3:49675281..49676977,2	K562	blood:

Variant related genes	Relation type
ENSG00000164062	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	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs1060962	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs10865955	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs11130192	1.00[JPT][hapmap]
rs11130199	0.83[GIH][hapmap];0.86[JPT][hapmap]
rs11130212	0.92[ASN][1000 genomes]
rs11130213	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1131095	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11709525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11710037	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11711485	0.95[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs11718165	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11720264	0.86[JPT][hapmap]
rs11720597	0.86[AMR][1000 genomes]
rs11917431	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919311	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11921590	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489092	0.86[JPT][hapmap]
rs13064576	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13085791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13316695	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1352890	0.97[ASN][1000 genomes]
rs1568661	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs1801143	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap]
rs1873626	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2131104	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs2131109	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs2172252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2329020	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2960548	0.82[ASN][1000 genomes]
rs3197999	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34762726	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];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35007338	0.87[ASN][1000 genomes]
rs35404120	0.87[ASN][1000 genomes]
rs35701831	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs3811697	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap]
rs3870338	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs3924462	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs4283605	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];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4625	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap]
rs4855839	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs4855847	0.87[ASN][1000 genomes]
rs4855852	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4855859	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs4855864	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs4855881	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4855884	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap]
rs6766131	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap]
rs6770670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6803222	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614725	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622302	0.83[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap]
rs7633271	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs7637999	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs7646366	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs885592	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9811982	1.00[CEU][hapmap]
rs9812791	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]
rs9822268	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9823546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9824092	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9827021	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9827708	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];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833611	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836291	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9837027	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap]
rs9837341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837520	0.89[ASN][1000 genomes]
rs9841110	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9853683	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs9858213	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap]
rs9858280	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap]
rs9858542	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9862080	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9875617	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs9882740	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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[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
rs1873625	IP6K2	cis	cerebellum	SCAN
rs1873625	CISH	cis	parietal	SCAN
rs1873625	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs1873625	RNF123	cis	cerebellum	SCAN
rs1873625	GPX1	cis	parietal	SCAN
rs1873625	PARP3	cis	parietal	SCAN
rs1873625	MYL3	cis	parietal	SCAN
rs1873625	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs1873625	FAM212A	cis	Muscle Skeletal	GTEx
rs1873625	NBEAL2	cis	cerebellum	SCAN
rs1873625	ZNF589	cis	parietal	SCAN
rs1873625	RNF123	cis	parietal	SCAN
rs1873625	CISH	cis	lymphoblastoid	seeQTL
rs1873625	RBM6	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49654400-49668200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:49655000-49668800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:49655600-49676200	Weak transcription	HepG2	liver
4	chr3:49657600-49685400	Weak transcription	Brain Substantia Nigra	brain
5	chr3:49660800-49682600	Weak transcription	Liver	Liver
6	chr3:49661000-49669200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:49661600-49692400	Weak transcription	Ovary	ovary
8	chr3:49661800-49682200	Weak transcription	Fetal Brain Male	brain
9	chr3:49662000-49667600	Strong transcription	Brain Germinal Matrix	brain
10	chr3:49662600-49668600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:49662800-49668400	Weak transcription	Lung	lung
12	chr3:49662800-49685000	Weak transcription	Right Ventricle	heart
13	chr3:49663600-49667000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:49663800-49679600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:49664200-49668200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:49664200-49669000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:49664200-49683200	Weak transcription	Pancreas	Pancrea
18	chr3:49664400-49668200	Weak transcription	NH-A	brain
19	chr3:49664600-49667800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:49664600-49674000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:49664600-49680000	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:49665000-49672400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:49665200-49667000	Weak transcription	Brain Anterior Caudate	brain
24	chr3:49665200-49668800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:49665600-49673800	Weak transcription	Brain Angular Gyrus	brain
26	chr3:49666800-49667400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:49666800-49667600	Genic enhancers	Fetal Brain Female	brain

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