Variant report

Variant	rs9844757
Chromosome Location	chr3:49343601-49343602
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49343579..49345278-chr3:49354855..49357707,2	K562	blood:

Variant related genes	Relation type
ENSG00000114316	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10049462	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1134043	0.93[CEU][hapmap]
rs11552724	1.00[CEU][hapmap]
rs11706189	1.00[CEU][hapmap]
rs11713297	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs11716445	0.92[CEU][hapmap]
rs11719220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs13068038	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs13077498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13321689	1.00[ASW][hapmap]
rs2230929	0.82[AFR][1000 genomes]
rs34343820	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34566463	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs35060561	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs3774800	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4855860	0.82[CEU][hapmap]
rs56306491	0.89[EUR][1000 genomes]
rs67831908	0.85[EUR][1000 genomes]
rs73084135	0.84[EUR][1000 genomes]
rs9311439	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9311440	1.00[ASW][hapmap];0.89[YRI][hapmap]
rs9814987	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs9818758	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs9837237	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs9837625	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs9839368	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs9847839	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs9870030	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9873994	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs9880088	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs9880309	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9990153	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs9844757	WDR6	cis	Artery Tibial	GTEx
rs9844757	HEMK1	cis	parietal	SCAN
rs9844757	WDR6	cis	Whole Blood	GTEx
rs9844757	ALAS1	cis	cerebellum	SCAN
rs9844757	RNF123	cis	parietal	SCAN
rs9844757	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9844757	WDR6	cis	Adipose Subcutaneous	GTEx
rs9844757	KBTBD3	trans	parietal	SCAN
rs9844757	WDR6	cis	Esophagus Mucosa	GTEx
rs9844757	ARIH2	cis	cerebellum	SCAN
rs9844757	WDR6	cis	cerebellum	SCAN
rs9844757	LRRC2	cis	cerebellum	SCAN
rs9844757	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9844757	C3orf62	cis	cerebellum	SCAN
rs9844757	CSPG5	cis	parietal	SCAN
rs9844757	NICN1	cis	cerebellum	SCAN
rs9844757	WDR6	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49312600-49375800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:49313200-49349400	Strong transcription	Dnd41	blood
3	chr3:49313600-49349200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:49314800-49355400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:49314800-49364800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:49315200-49349600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:49315200-49349600	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:49315200-49352600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:49315200-49373600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:49315200-49375000	Strong transcription	Fetal Stomach	stomach
11	chr3:49315400-49370400	Strong transcription	Fetal Thymus	thymus
12	chr3:49315800-49349200	Strong transcription	Fetal Brain Female	brain
13	chr3:49316200-49370200	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:49317200-49349400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr3:49317200-49371800	Strong transcription	Fetal Intestine Small	intestine
16	chr3:49317400-49349200	Strong transcription	Fetal Intestine Large	intestine
17	chr3:49317400-49349600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:49317400-49369400	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:49317400-49370600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:49319200-49374800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:49319400-49349600	Strong transcription	Liver	Liver
22	chr3:49319600-49344000	Strong transcription	Osteobl	bone
23	chr3:49319600-49349400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:49319600-49371800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:49319800-49349200	Strong transcription	Brain Germinal Matrix	brain
26	chr3:49319800-49349400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:49320000-49349000	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:49320000-49349600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:49320200-49375000	Strong transcription	Thymus	Thymus
30	chr3:49320600-49351400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:49320800-49344200	Strong transcription	Primary B cells from cord blood	blood
32	chr3:49320800-49349200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:49320800-49349400	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:49320800-49368000	Strong transcription	Primary T cells from cord blood	blood
35	chr3:49321000-49348400	Strong transcription	NH-A	brain
36	chr3:49321800-49373600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr3:49326800-49373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:49326800-49375000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:49329400-49344000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr3:49332400-49351400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:49332600-49354400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:49333600-49369600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr3:49334200-49349000	Strong transcription	Fetal Lung	lung
44	chr3:49334200-49349200	Strong transcription	Brain Cingulate Gyrus	brain
45	chr3:49334600-49345800	Strong transcription	Brain Anterior Caudate	brain
46	chr3:49334800-49349200	Strong transcription	Brain Hippocampus Middle	brain
47	chr3:49335000-49349200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr3:49335000-49349200	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr3:49335000-49351000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:49335000-49365200	Strong transcription	Spleen	Spleen

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