Variant report

Variant	rs1973480
Chromosome Location	chr6:74511980-74511981
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:74511500..74515522-chr6:74517572..74520976,4	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10498895	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10943129	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12203043	0.83[MEX][hapmap]
rs12662725	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1392913	0.81[CEU][hapmap];0.80[GIH][hapmap]
rs17760906	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2033736	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2047670	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2118330	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2118331	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2118332	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2164755	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2351527	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2351528	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4342388	0.84[CEU][hapmap]
rs4706555	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4706556	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4708082	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4708083	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4708088	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5023688	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6453698	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6453699	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6453700	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6917630	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6918612	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6921996	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6922211	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6932012	0.84[CEU][hapmap]
rs7738437	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7742435	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7748237	0.84[ASN][1000 genomes]
rs7748871	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7762080	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7762433	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7762638	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7763367	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7771585	0.88[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7774119	0.83[MEX][hapmap]
rs7776411	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9293940	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9293941	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9442955	0.82[CEU][hapmap]
rs9442956	0.83[MEX][hapmap]
rs9442960	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9442961	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9442963	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9447014	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9447015	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9447016	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9447017	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9447019	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9447025	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9447027	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9447029	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
2	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
3	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
4	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
5	nsv463154	chr6:74412048-74775904	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv603695	chr6:74412048-74775904	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1973480	COL21A1	trans	cerebellum	SCAN
rs1973480	SLC17A5	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74438400-74527200	Weak transcription	Esophagus	oesophagus
2	chr6:74441400-74544400	Weak transcription	Aorta	Aorta
3	chr6:74475200-74513600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:74477400-74543400	Weak transcription	Lung	lung
5	chr6:74484600-74542000	Weak transcription	Right Ventricle	heart
6	chr6:74484800-74512600	Weak transcription	HSMM	muscle
7	chr6:74490400-74527800	Weak transcription	Thymus	Thymus
8	chr6:74494400-74530800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr6:74495400-74533200	Weak transcription	Fetal Stomach	stomach
10	chr6:74496800-74528800	Weak transcription	Dnd41	blood
11	chr6:74499000-74527000	Weak transcription	Fetal Thymus	thymus
12	chr6:74499000-74532600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:74499200-74520200	Weak transcription	NHEK	skin
14	chr6:74500600-74525800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:74500600-74527600	Weak transcription	Primary T cells from cord blood	blood
16	chr6:74501200-74514000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:74501200-74521600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:74503200-74520600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:74503400-74520400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr6:74503400-74521600	Weak transcription	Left Ventricle	heart
21	chr6:74503400-74530600	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:74503600-74520800	Weak transcription	Adipose Nuclei	Adipose
23	chr6:74503800-74526600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:74506200-74513600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:74508600-74513600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:74508600-74514000	Weak transcription	HMEC	breast
27	chr6:74508600-74516400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:74508600-74533000	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:74508800-74512600	Weak transcription	Hela-S3	cervix
30	chr6:74508800-74512600	Weak transcription	NH-A	brain
31	chr6:74509000-74512000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr6:74509000-74516600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr6:74509800-74513400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:74510000-74512600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:74510000-74513000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:74510000-74513600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:74510000-74513600	Weak transcription	Placenta	Placenta
38	chr6:74510200-74512400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:74510200-74514200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:74510400-74512600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:74510600-74514200	Enhancers	Liver	Liver
42	chr6:74510600-74514400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:74510800-74514000	Enhancers	A549	lung
44	chr6:74510800-74514200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:74510800-74514400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:74511000-74512600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:74511000-74527200	Weak transcription	Fetal Lung	lung
48	chr6:74511200-74512600	Weak transcription	HUVEC	blood vessel
49	chr6:74511200-74512800	Enhancers	NHDF-Ad	bronchial
50	chr6:74511400-74514400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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