Variant report

Variant	rs13324142
Chromosome Location	chr3:48669447-48669448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48669378-48669464	MCF-7	breast:	n/a	n/a
2	POLR2A	chr3:48667295-48670885	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:48669292-48669704	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr3:48669135-48669551	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48644319..48649140-chr3:48667292..48673836,7	K562	blood:
2	chr3:48669152..48670983-chr3:48700604..48702658,2	MCF-7	breast:
3	chr3:48514107..48516088-chr3:48667675..48669788,2	K562	blood:
4	chr3:48667529..48675453-chr3:48697968..48703139,10	MCF-7	breast:
5	chr3:48634583..48638851-chr3:48666607..48670894,4	MCF-7	breast:

No data

Variant related genes	Relation type
SLC26A6	TF binding region
ENSG00000008300	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000010256	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1003649	0.83[GIH][hapmap]
rs10470687	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs11706983	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs11708786	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs11713694	0.83[GIH][hapmap]
rs11719291	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs12107252	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12107418	0.90[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12715429	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13060933	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13062576	0.82[CHB][hapmap]
rs13063312	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13070798	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13074318	0.83[GIH][hapmap]
rs13076269	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13091944	1.00[JPT][hapmap]
rs13096357	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13319651	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13324119	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13434258	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs17080289	0.90[CHD][hapmap];1.00[GIH][hapmap]
rs2006871	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2276850	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];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276852	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2286651	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2286652	1.00[ASW][hapmap];0.90[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2302295	0.88[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2310996	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2310997	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28452701	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2854394	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs34037363	0.83[GIH][hapmap]
rs34096717	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34368826	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34638686	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35064573	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs35343040	0.81[ASN][1000 genomes]
rs3733086	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3806694	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3821875	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3821876	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3895736	0.85[LWK][hapmap];0.85[MKK][hapmap]
rs3969942	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs57334642	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768448	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6773261	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6781283	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6792156	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6792525	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs68042649	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6806059	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs73078349	0.82[EUR][1000 genomes]
rs740787	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7428949	1.00[JPT][hapmap]
rs7620853	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7631574	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9809222	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9810549	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9810991	0.89[CHD][hapmap];0.83[GIH][hapmap]
rs9811318	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]
rs9812200	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9821797	0.90[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9830581	0.84[ASW][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9836462	0.90[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9837687	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9841602	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]
rs9843316	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9850102	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9851771	0.83[GIH][hapmap]
rs9868809	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9869698	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9871180	0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9873726	0.86[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9875911	0.83[GIH][hapmap]
rs9878063	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9878950	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9881877	0.85[CHD][hapmap];1.00[GIH][hapmap]
rs9882549	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs9882962	0.80[CHD][hapmap];0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	esv3430072	chr3:48668048-48673146	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13324142	WDR6	cis	multi-tissue	Pritchard
rs13324142	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs13324142	WDR6	cis	lymphoblastoid	seeQTL
rs13324142	WDR6	cis	Adipose Subcutaneous	GTEx
rs13324142	WDR6	cis	Esophagus Mucosa	GTEx
rs13324142	USP4	cis	multi-tissue	Pritchard
rs13324142	SLC26A6	cis	lung	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48649000-48672000	Weak transcription	Fetal Brain Male	brain
2	chr3:48656400-48671400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:48657800-48670000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:48659000-48671200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:48660000-48671200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:48661000-48671200	Strong transcription	Aorta	Aorta
7	chr3:48661000-48671600	Weak transcription	Psoas Muscle	Psoas
8	chr3:48661200-48670200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:48661200-48670800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:48661200-48671000	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr3:48661200-48671800	Weak transcription	Small Intestine	intestine
12	chr3:48661600-48670600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:48661600-48670800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:48661600-48670800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:48661600-48670800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:48661600-48670800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr3:48661600-48670800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:48661600-48671200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:48661600-48671400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:48661800-48670200	Strong transcription	Spleen	Spleen
21	chr3:48661800-48670800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:48661800-48671000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:48661800-48671400	Strong transcription	NHEK	skin
24	chr3:48661800-48671600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:48662000-48671000	Strong transcription	Brain Hippocampus Middle	brain
26	chr3:48662000-48671000	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:48662000-48671200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr3:48662000-48671200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:48662000-48671400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:48662000-48671400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr3:48662000-48671800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr3:48662200-48670200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr3:48662200-48670600	Strong transcription	Osteobl	bone
34	chr3:48662200-48670800	Strong transcription	Thymus	Thymus
35	chr3:48662200-48671000	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:48662200-48671200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:48662200-48671200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:48662200-48671400	Strong transcription	Fetal Intestine Small	intestine
39	chr3:48662200-48671400	Strong transcription	Fetal Stomach	stomach
40	chr3:48662200-48671800	Weak transcription	Primary B cells from cord blood	blood
41	chr3:48662200-48671800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:48662400-48670600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:48662400-48670800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:48662400-48671200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:48662400-48671200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr3:48662400-48671200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:48662400-48671200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr3:48662400-48671200	Strong transcription	Fetal Intestine Large	intestine
49	chr3:48662400-48671200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr3:48662400-48671400	Strong transcription	NHLF	lung

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