Variant report

Variant	rs3800091
Chromosome Location	chr6:1837828-1837829
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1612565..1615275-chr6:1837590..1839107,2	MCF-7	breast:
2	chr6:1831250..1835471-chr6:1835503..1841068,8	MCF-7	breast:
3	chr6:1762522..1764369-chr6:1837443..1839225,2	MCF-7	breast:
4	chr6:1608467..1612521-chr6:1837362..1840946,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1467594	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1543538	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1570533	0.82[CEU][hapmap];0.82[TSI][hapmap]
rs1570535	0.84[ASW][hapmap]
rs2281760	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2296131	0.92[CEU][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes]
rs3778537	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778538	0.96[EUR][1000 genomes]
rs3778540	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3800097	0.92[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3800099	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs3800100	0.84[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3800102	0.95[CEU][hapmap]
rs3800103	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3800104	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3800106	0.88[CEU][hapmap]
rs3800107	0.96[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800108	0.88[CEU][hapmap]
rs3800115	0.92[CEU][hapmap]
rs3800121	0.89[CEU][hapmap]
rs3800122	0.82[CEU][hapmap];0.84[TSI][hapmap]
rs3823277	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4959160	0.84[ASW][hapmap]
rs4959613	0.89[ASN][1000 genomes]
rs6940806	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9328073	0.88[CEU][hapmap]
rs9378661	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs9391935	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9392342	0.89[CEU][hapmap]
rs9405152	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv538094	chr6:1757776-1907505	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
9	nsv883383	chr6:1775436-1918572	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv883384	chr6:1787862-1942538	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1019895	chr6:1832936-1882435	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3800091	WNT3A	trans	lymphoblastoid	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1829800-1856600	Weak transcription	Primary T cells from cord blood	blood
2	chr6:1831800-1838000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:1833000-1840000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr6:1833400-1838000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:1833400-1838000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:1833400-1843800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:1833400-1845800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:1833400-1856600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:1833600-1838000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:1833600-1838000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:1833600-1838400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:1833600-1838400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr6:1833600-1839400	Weak transcription	Aorta	Aorta
14	chr6:1833600-1839400	Weak transcription	Stomach Mucosa	stomach
15	chr6:1833600-1840000	Weak transcription	Pancreas	Pancrea
16	chr6:1833600-1840400	Weak transcription	Osteobl	bone
17	chr6:1833600-1842000	Weak transcription	Left Ventricle	heart
18	chr6:1833600-1842000	Weak transcription	Right Atrium	heart
19	chr6:1833600-1842400	Weak transcription	Gastric	stomach
20	chr6:1833600-1843000	Weak transcription	Fetal Intestine Small	intestine
21	chr6:1833600-1845800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:1833600-1846000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:1833600-1849600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:1833800-1838000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:1833800-1838000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:1833800-1838000	Weak transcription	Adipose Nuclei	Adipose
27	chr6:1833800-1838000	Weak transcription	NH-A	brain
28	chr6:1833800-1838200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:1833800-1839200	Weak transcription	Liver	Liver
30	chr6:1833800-1842000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:1834000-1848000	Weak transcription	HepG2	liver
32	chr6:1834200-1838000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:1834800-1838000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:1835600-1838000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:1835600-1845800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:1835800-1838800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:1836600-1839400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:1836600-1839800	Enhancers	Fetal Kidney	kidney
39	chr6:1836800-1838400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr6:1837200-1839400	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr6:1837600-1838400	Enhancers	H9 Cell Line	embryonic stem cell
42	chr6:1837600-1838800	Enhancers	Fetal Brain Male	brain
43	chr6:1837600-1839200	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr6:1837600-1839400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:1837600-1839400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:1837600-1839600	Enhancers	Brain Germinal Matrix	brain
47	chr6:1837600-1840000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:1837600-1840000	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr6:1837600-1840000	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr6:1837800-1838200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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