Variant report

Variant	rs1568350
Chromosome Location	chr3:135648685-135648686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:57920511..57922569-chr3:135647272..135648879,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:115)

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];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10935175	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13072596	0.82[EUR][1000 genomes]
rs13082684	0.92[ASN][1000 genomes]
rs13097946	0.82[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs13098245	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs13322891	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325914	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs13434196	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1356664	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1401545	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403766	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403767	1.00[ASN][1000 genomes]
rs1403770	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1568349	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16843509	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17196987	0.81[EUR][1000 genomes]
rs17197552	0.82[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs17250445	0.81[EUR][1000 genomes]
rs2204259	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28449384	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28570106	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28576629	0.92[ASN][1000 genomes]
rs28855968	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28875187	1.00[ASN][1000 genomes]
rs34311570	0.80[EUR][1000 genomes]
rs34522617	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34767379	0.92[ASN][1000 genomes]
rs35257855	0.81[EUR][1000 genomes]
rs35722356	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36039354	0.92[ASN][1000 genomes]
rs4073308	0.85[CEU][hapmap]
rs4718	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55678980	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56308637	1.00[ASN][1000 genomes]
rs56807950	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59063369	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66544356	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6771997	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6773469	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6774289	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6775778	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6779603	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6786769	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs6802139	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6807058	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6807242	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6807565	0.92[ASN][1000 genomes]
rs6809006	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6810223	0.81[EUR][1000 genomes]
rs73222222	0.92[ASN][1000 genomes]
rs7427833	0.92[ASN][1000 genomes]
rs7433567	0.86[CEU][hapmap];0.92[ASN][1000 genomes]
rs7609938	0.85[AMR][1000 genomes];0.95[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];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7621425	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs7626676	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7628848	0.92[ASN][1000 genomes]
rs7638129	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7640153	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7641070	0.92[ASN][1000 genomes]
rs7643661	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs870812	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs908825	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289502	0.80[EUR][1000 genomes]
rs9289503	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9808979	0.81[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs9812561	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9813082	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9814505	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814557	0.82[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9819440	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819988	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9820189	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824558	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9825239	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9826806	0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs9829329	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9829476	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9833699	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833799	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9834104	0.80[EUR][1000 genomes]
rs9834624	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836374	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9836758	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9837855	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839259	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9842840	1.00[JPT][hapmap]
rs9842864	0.92[ASN][1000 genomes]
rs9843725	0.82[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9844478	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9846137	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs9848322	0.82[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9849088	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9851361	0.80[EUR][1000 genomes]
rs9853577	0.82[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs9854494	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862264	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9862743	0.82[EUR][1000 genomes]
rs9862763	0.81[EUR][1000 genomes]
rs9862777	0.92[ASN][1000 genomes]
rs9864247	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9864514	0.80[EUR][1000 genomes]
rs9864656	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9864775	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868246	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs9870581	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872542	0.82[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs9875948	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876837	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9877722	0.98[AMR][1000 genomes];0.95[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
rs1568350	PRR23C	cis	parietal	SCAN
rs1568350	TMEM22	cis	cerebellum	SCAN
rs1568350	PPP2R3A	cis	cerebellum	SCAN
rs1568350	MSL2	cis	cerebellum	SCAN
rs1568350	CRYBB2	trans	lymphoblastoid	seeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135646200-135648800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:135647800-135649400	Enhancers	Fetal Muscle Leg	muscle
3	chr3:135648000-135649200	Enhancers	Brain Hippocampus Middle	brain
4	chr3:135648000-135649400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:135648000-135649400	Enhancers	Duodenum Smooth Muscle	Duodenum
6	chr3:135648000-135649400	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr3:135648000-135649400	Enhancers	NHDF-Ad	bronchial
8	chr3:135648000-135649600	Enhancers	Colon Smooth Muscle	Colon
9	chr3:135648000-135649600	Enhancers	Rectal Smooth Muscle	rectum
10	chr3:135648000-135649600	Enhancers	HSMMtube	muscle
11	chr3:135648200-135649200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:135648200-135649200	Weak transcription	Psoas Muscle	Psoas
13	chr3:135648400-135648800	Enhancers	Stomach Smooth Muscle	stomach
14	chr3:135648400-135649000	Enhancers	Fetal Heart	heart
15	chr3:135648400-135649200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:135648400-135649200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:135648400-135649200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr3:135648400-135649200	Enhancers	NHEK	skin
19	chr3:135648400-135649400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:135648400-135649400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:135648400-135649400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:135648400-135649600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr3:135648400-135649600	Enhancers	HSMM	muscle
24	chr3:135648600-135648800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr3:135648600-135649000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:135648600-135649200	Enhancers	Brain Angular Gyrus	brain
27	chr3:135648600-135649400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:135648600-135649400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:135648600-135649400	Enhancers	Brain Substantia Nigra	brain
30	chr3:135648600-135649400	Enhancers	Fetal Stomach	stomach
31	chr3:135648600-135649400	Enhancers	Right Ventricle	heart
32	chr3:135648600-135649400	Enhancers	HMEC	breast

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