Variant report

Variant	rs9875948
Chromosome Location	chr3:135641904-135641905
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	chr3:135639960..135642510-chr3:135644170..135646258,2	K562	blood:
2	chr3:135641417..135644037-chr3:135644616..135646188,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242222	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10048942	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10049233	0.92[ASN][1000 genomes]
rs10512981	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10935175	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13082684	0.92[ASN][1000 genomes]
rs13097946	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs13098245	1.00[JPT][hapmap]
rs13322891	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325914	1.00[JPT][hapmap]
rs13434196	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1356664	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1401545	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403766	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403767	1.00[ASN][1000 genomes]
rs1403770	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1568349	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1568350	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843509	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17197552	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs2204259	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28449384	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28570106	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28576629	0.92[ASN][1000 genomes]
rs28855968	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28875187	1.00[ASN][1000 genomes]
rs34522617	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs34767379	0.92[ASN][1000 genomes]
rs35722356	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36039354	0.92[ASN][1000 genomes]
rs4073308	0.85[CEU][hapmap]
rs4718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55678980	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56308637	1.00[ASN][1000 genomes]
rs56807950	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59063369	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66544356	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6771997	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6773469	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6774289	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6775778	1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs6779603	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6786769	0.82[CEU][hapmap]
rs6802139	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6807058	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6807242	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6807565	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6809006	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs73222222	0.92[ASN][1000 genomes]
rs7427833	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7433567	0.86[CEU][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7609938	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7621331	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs7621396	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7621425	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs7626676	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7628848	0.92[ASN][1000 genomes]
rs7638129	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7640153	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7641070	0.92[ASN][1000 genomes]
rs7643661	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs870812	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs908825	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289503	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9808979	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs9812561	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9813082	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9814505	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814557	0.84[ASW][hapmap];0.82[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9819440	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819988	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9820189	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824558	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9825239	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9826806	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs9829329	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9829476	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9833699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833799	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9834624	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836374	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9836758	1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs9837855	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839259	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9842840	1.00[JPT][hapmap]
rs9842864	0.92[ASN][1000 genomes]
rs9843725	0.84[ASW][hapmap];0.82[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9844478	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9846137	0.86[CEU][hapmap]
rs9848322	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9849088	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9853577	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes]
rs9854494	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862264	1.00[JPT][hapmap]
rs9862777	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9864247	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9864656	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9864775	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868246	0.86[CEU][hapmap]
rs9870581	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872542	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9876837	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9877722	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883808	0.86[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9875948	PRR23C	cis	parietal	SCAN
rs9875948	TMEM22	cis	cerebellum	SCAN
rs9875948	PPP2R3A	cis	cerebellum	SCAN
rs9875948	MSL2	cis	cerebellum	SCAN
rs9875948	CRYBB2	trans	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135640600-135642200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:135640600-135642400	Enhancers	HMEC	breast
3	chr3:135640600-135643400	Weak transcription	Pancreas	Pancrea
4	chr3:135640800-135642200	Enhancers	NHEK	skin
5	chr3:135641200-135642000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:135641200-135645800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:135641400-135642000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:135641400-135642200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:135641600-135642000	Enhancers	NHDF-Ad	bronchial
10	chr3:135641600-135642200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:135641600-135642200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:135641800-135642000	Enhancers	Placenta	Placenta
13	chr3:135641800-135645600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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