Variant report

Variant	rs9841602
Chromosome Location	chr3:48713570-48713571
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48708500..48710574-chr3:48712082..48713667,2	K562	blood:
2	chr3:48710449..48713681-chr3:48721332..48723160,4	K562	blood:
3	chr3:48698129..48704726-chr3:48706101..48715056,13	MCF-7	breast:
4	chr3:48713537..48717616-chr3:48720627..48724588,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228350	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000271973	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1003649	0.83[GIH][hapmap]
rs10470687	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs11557629	0.85[EUR][1000 genomes]
rs11706203	0.82[EUR][1000 genomes]
rs11706983	1.00[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs11708786	1.00[GIH][hapmap]
rs11713694	0.83[GIH][hapmap]
rs11719291	1.00[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs12107252	0.82[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];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12107418	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12497850	0.83[ASW][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs12715429	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060933	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13063223	0.82[EUR][1000 genomes]
rs13063312	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13070798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074318	0.83[GIH][hapmap]
rs13076269	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13090013	0.85[EUR][1000 genomes]
rs13091944	1.00[JPT][hapmap]
rs13096357	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13316551	0.82[EUR][1000 genomes]
rs13319651	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13324119	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324142	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13434258	1.00[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs1352420	0.83[YRI][hapmap]
rs17080289	0.80[CHD][hapmap];1.00[GIH][hapmap]
rs17080319	0.85[EUR][1000 genomes]
rs2006871	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2276850	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2276852	0.90[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2286651	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2286652	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2302295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2310996	0.82[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2310997	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28452701	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2854394	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs28567949	0.85[EUR][1000 genomes]
rs28657585	0.83[EUR][1000 genomes]
rs34037363	0.83[GIH][hapmap]
rs34096717	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34153629	0.85[EUR][1000 genomes]
rs34368826	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34577723	0.83[EUR][1000 genomes]
rs34638686	0.80[EUR][1000 genomes]
rs35064573	1.00[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs3733086	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821875	0.81[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821876	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3969942	0.83[GIH][hapmap]
rs4858798	1.00[YRI][hapmap]
rs4858828	1.00[YRI][hapmap]
rs4858831	1.00[YRI][hapmap]
rs57334642	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6768448	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773261	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6781283	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6788650	1.00[YRI][hapmap]
rs6792156	0.94[ASW][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6792525	0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs68042649	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806059	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs73078362	0.82[EUR][1000 genomes]
rs740787	0.89[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7428949	1.00[JPT][hapmap]
rs7620853	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7631574	0.82[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9809222	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810549	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9810991	0.83[GIH][hapmap]
rs9811027	0.85[EUR][1000 genomes]
rs9811318	0.94[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];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812200	0.89[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];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812977	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9821797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830581	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9836462	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];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837687	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9843316	0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9850102	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9851771	0.83[GIH][hapmap]
rs9854034	0.82[EUR][1000 genomes]
rs9868809	0.81[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.81[EUR][1000 genomes]
rs9869698	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9871180	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9873726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875911	0.83[GIH][hapmap]
rs9877542	0.82[EUR][1000 genomes]
rs9877685	0.82[EUR][1000 genomes]
rs9878063	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9878950	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9881877	1.00[GIH][hapmap]
rs9882549	1.00[GIH][hapmap];0.82[EUR][1000 genomes]
rs9882962	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9841602	WDR6	cis	lymphoblastoid	seeQTL
rs9841602	WDR6	cis	Esophagus Mucosa	GTEx
rs9841602	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9841602	WDR6	cis	Adipose Subcutaneous	GTEx
rs9841602	WDR6	cis	lung	GTEx
rs9841602	WDR6	cis	Artery Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48701200-48721000	Weak transcription	Fetal Brain Male	brain
2	chr3:48701600-48715400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:48701600-48716800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:48701600-48718000	Weak transcription	NHDF-Ad	bronchial
5	chr3:48701600-48720800	Weak transcription	Right Atrium	heart
6	chr3:48701600-48720800	Weak transcription	HUVEC	blood vessel
7	chr3:48701800-48714800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:48701800-48715200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:48701800-48715200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:48701800-48715600	Weak transcription	NH-A	brain
11	chr3:48701800-48715800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:48701800-48715800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:48701800-48716800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:48701800-48721400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:48702000-48716800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:48702000-48716800	Weak transcription	HSMMtube	muscle
17	chr3:48702000-48721400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:48702200-48717000	Weak transcription	K562	blood
19	chr3:48702600-48715000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:48702800-48714800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:48702800-48717000	Weak transcription	Fetal Heart	heart
22	chr3:48703200-48715200	Weak transcription	Stomach Mucosa	stomach
23	chr3:48703400-48715600	Weak transcription	Fetal Lung	lung
24	chr3:48703600-48715600	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:48704400-48716000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:48705800-48720600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:48707200-48715000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:48707200-48721400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:48708200-48714400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:48708200-48720200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:48708200-48720200	Strong transcription	Fetal Brain Female	brain
32	chr3:48708200-48720600	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:48708200-48720600	Strong transcription	Fetal Intestine Small	intestine
34	chr3:48708200-48720600	Strong transcription	Fetal Stomach	stomach
35	chr3:48708200-48721000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:48708400-48714400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:48708400-48715000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:48708400-48720400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:48708400-48720400	Strong transcription	Brain Germinal Matrix	brain
40	chr3:48708400-48720400	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr3:48708400-48720800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:48708400-48721000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:48708600-48720600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:48708800-48720600	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr3:48709000-48716800	Weak transcription	A549	lung
46	chr3:48709000-48721600	Weak transcription	Psoas Muscle	Psoas
47	chr3:48709200-48714600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:48709200-48715600	Weak transcription	Colonic Mucosa	Colon
49	chr3:48709200-48720200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr3:48709800-48715000	Weak transcription	Primary T cells fromperipheralblood	blood

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