Variant report

Variant	rs9882549
Chromosome Location	chr3:48749358-48749359
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48731283..48735780-chr3:48749291..48752542,4	MCF-7	breast:
2	chr3:48699198..48701664-chr3:48748903..48750762,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068745	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000008300	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs1003649	0.83[GIH][hapmap]
rs10470687	0.83[GIH][hapmap]
rs1048940	0.84[CEU][hapmap]
rs10780033	1.00[CHD][hapmap]
rs10865952	0.95[ASN][1000 genomes]
rs11130176	1.00[CHD][hapmap]
rs11557629	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706203	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708022	0.84[AMR][1000 genomes]
rs11708786	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709092	0.80[AMR][1000 genomes]
rs11709246	0.84[AMR][1000 genomes]
rs11713694	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs11715177	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715689	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11715713	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11715835	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11719291	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920534	1.00[CHD][hapmap]
rs11928552	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12107252	1.00[GIH][hapmap]
rs12107418	1.00[GIH][hapmap]
rs12493289	1.00[JPT][hapmap]
rs12493578	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12497850	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12715429	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13060933	0.83[GIH][hapmap]
rs13063223	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063312	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs13070798	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13073997	0.84[AMR][1000 genomes]
rs13074318	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs13084000	0.84[AMR][1000 genomes]
rs13087930	0.84[AMR][1000 genomes]
rs13090013	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094900	0.80[AMR][1000 genomes]
rs13316551	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13319651	0.83[GIH][hapmap]
rs13324119	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13324142	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs13324950	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352420	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17080289	1.00[GIH][hapmap]
rs17080319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006871	0.83[GIH][hapmap]
rs2276850	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs2276852	1.00[GIH][hapmap]
rs2286651	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2286652	1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2302295	0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2310996	1.00[GIH][hapmap]
rs28452701	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2854394	0.83[GIH][hapmap]
rs28567949	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28657585	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28793701	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34037363	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap]
rs34096717	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34153629	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34477108	0.84[AMR][1000 genomes]
rs34509487	0.84[AMR][1000 genomes]
rs34577723	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35064573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733086	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs3821875	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3821876	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs3969942	0.83[GIH][hapmap]
rs4077495	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858798	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4858828	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4858831	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4974079	1.00[CHD][hapmap]
rs4974085	1.00[CHD][hapmap]
rs4974087	1.00[CHD][hapmap]
rs56735597	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61137521	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6442130	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs67060340	0.80[AMR][1000 genomes]
rs67332931	0.84[AMR][1000 genomes]
rs6768448	0.82[EUR][1000 genomes]
rs6781283	0.83[GIH][hapmap]
rs6788650	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6791542	1.00[CHD][hapmap]
rs6792156	1.00[GIH][hapmap]
rs6792525	0.83[GIH][hapmap]
rs68042649	0.82[EUR][1000 genomes]
rs6806059	0.83[GIH][hapmap]
rs71324924	0.84[AMR][1000 genomes]
rs740787	1.00[GIH][hapmap]
rs7430501	1.00[CHD][hapmap]
rs7431710	1.00[CHD][hapmap]
rs7431857	1.00[CHD][hapmap]
rs7623023	1.00[CHD][hapmap]
rs7627404	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7631574	1.00[GIH][hapmap]
rs7633840	0.86[ASN][1000 genomes]
rs7647813	1.00[CHD][hapmap]
rs7649458	1.00[CHD][hapmap]
rs9311430	1.00[CHD][hapmap]
rs9311433	1.00[CHD][hapmap]
rs9311434	1.00[CHD][hapmap]
rs9682444	0.87[CHD][hapmap]
rs9755490	0.87[CHD][hapmap]
rs9809222	0.82[EUR][1000 genomes]
rs9810549	0.83[GIH][hapmap]
rs9810991	0.83[GIH][hapmap]
rs9811027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811318	1.00[GIH][hapmap];0.82[EUR][1000 genomes]
rs9812200	1.00[GIH][hapmap]
rs9821797	0.82[EUR][1000 genomes]
rs9830581	1.00[GIH][hapmap]
rs9834996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835307	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9836462	1.00[GIH][hapmap];0.82[EUR][1000 genomes]
rs9837687	0.83[GIH][hapmap]
rs9841602	1.00[GIH][hapmap];0.82[EUR][1000 genomes]
rs9843316	1.00[GIH][hapmap]
rs9848203	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9850102	0.83[GIH][hapmap]
rs9854034	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9868809	0.83[GIH][hapmap]
rs9869698	0.83[GIH][hapmap]
rs9871180	1.00[GIH][hapmap]
rs9873726	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9876848	1.00[CHD][hapmap]
rs9877542	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878950	0.83[GIH][hapmap]
rs9881877	1.00[GIH][hapmap]
rs9882962	0.83[GIH][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	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs9882549	WDR6	cis	Esophagus Mucosa	GTEx
rs9882549	NCKIPSD	cis	parietal	SCAN
rs9882549	C3orf62	cis	cerebellum	SCAN
rs9882549	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs9882549	WDR6	cis	lymphoblastoid	seeQTL
rs9882549	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9882549	WDR6	cis	Adipose Subcutaneous	GTEx
rs9882549	CSPG5	cis	parietal	SCAN
rs9882549	WDR6	cis	parietal	SCAN
rs9882549	WDR6	cis	lung	GTEx
rs9882549	RNF123	cis	parietal	SCAN
rs9882549	C3orf62	cis	parietal	SCAN
rs9882549	ALAS1	cis	cerebellum	SCAN
rs9882549	LRRC2	cis	cerebellum	SCAN
rs9882549	WDR6	cis	cerebellum	SCAN
rs9882549	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48733000-48753400	Weak transcription	Aorta	Aorta
2	chr3:48738200-48752400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:48739800-48750800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:48740000-48753600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:48741400-48750600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:48741600-48749600	Strong transcription	Primary B cells from cord blood	blood
7	chr3:48741600-48750600	Strong transcription	Fetal Muscle Trunk	muscle
8	chr3:48741600-48752400	Strong transcription	Fetal Intestine Large	intestine
9	chr3:48741800-48749400	Strong transcription	Fetal Stomach	stomach
10	chr3:48741800-48751800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr3:48741800-48752400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:48741800-48752600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:48742800-48750000	Strong transcription	Placenta	Placenta
14	chr3:48742800-48750800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:48743000-48749600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:48743000-48752400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:48743000-48753000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:48743600-48750600	Strong transcription	Hela-S3	cervix
19	chr3:48743600-48751200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr3:48743600-48751800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
21	chr3:48743600-48752000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:48743800-48752800	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chr3:48744600-48749400	Strong transcription	Liver	Liver
24	chr3:48744600-48749600	Strong transcription	HUVEC	blood vessel
25	chr3:48744600-48751000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:48744600-48751200	Genic enhancers	Primary T cells from cord blood	blood
27	chr3:48744800-48750600	Genic enhancers	Brain Germinal Matrix	brain
28	chr3:48745600-48751200	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr3:48745600-48752800	Weak transcription	Small Intestine	intestine
30	chr3:48745800-48753400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr3:48746400-48749800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
32	chr3:48746600-48752400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:48746600-48752400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:48746600-48752600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:48746800-48749400	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr3:48746800-48750000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:48746800-48750600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:48746800-48750600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:48746800-48750600	Strong transcription	Fetal Intestine Small	intestine
40	chr3:48746800-48750600	Strong transcription	Fetal Lung	lung
41	chr3:48746800-48752200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr3:48746800-48752200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:48747000-48749400	Strong transcription	Fetal Thymus	thymus
44	chr3:48747000-48750000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr3:48747000-48750600	Strong transcription	Stomach Smooth Muscle	stomach
46	chr3:48747000-48751800	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:48747000-48751800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:48747000-48752200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:48747000-48752200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:48747000-48752600	Weak transcription	A549	lung

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