Variant report

Variant	rs9872542
Chromosome Location	chr3:135720673-135720674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10048942	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10049233	0.84[ASN][1000 genomes]
rs10512973	1.00[CHB][hapmap]
rs10512981	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10935175	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13072596	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082684	0.84[ASN][1000 genomes]
rs13097946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098245	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325914	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434196	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1403766	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1403770	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1523595	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523596	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523597	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568349	0.93[ASN][1000 genomes]
rs1568350	0.80[EUR][1000 genomes]
rs16843509	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17196987	1.00[GIH][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17197552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17250445	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2204259	0.82[CEU][hapmap];0.93[ASN][1000 genomes]
rs28449384	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28576629	0.84[ASN][1000 genomes]
rs34311570	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34409306	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34522617	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34767379	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35257855	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36039354	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4073308	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56807950	0.93[ASN][1000 genomes]
rs59063369	0.93[ASN][1000 genomes]
rs66544356	0.93[ASN][1000 genomes]
rs67039922	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771224	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773469	0.93[ASN][1000 genomes]
rs6774289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775778	1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs6779603	0.93[ASN][1000 genomes]
rs6786769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802139	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6803447	1.00[CHB][hapmap]
rs6807058	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6807242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807565	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6809006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810223	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71336046	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73222222	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7427833	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7433567	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7609938	0.93[ASN][1000 genomes]
rs7621331	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621396	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7621425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626676	0.93[ASN][1000 genomes]
rs7628848	0.84[ASN][1000 genomes]
rs7638129	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7640153	0.93[ASN][1000 genomes]
rs7641070	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7643661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289502	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808979	0.95[CEU][hapmap];1.00[CHB][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]
rs9812561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813082	0.93[ASN][1000 genomes]
rs9814557	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9819988	0.93[ASN][1000 genomes]
rs9824558	0.93[ASN][1000 genomes]
rs9825239	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9826806	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829329	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9829476	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9833470	1.00[CHB][hapmap]
rs9833799	0.93[ASN][1000 genomes]
rs9834104	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834624	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9836374	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836758	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9837355	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9839259	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9842840	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842864	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9843725	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9844478	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9846137	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848322	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9849088	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9851361	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853577	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9854494	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9862264	0.95[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862743	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9862763	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862777	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9864247	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9864514	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864656	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9864775	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs9868246	0.95[CEU][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870581	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9875328	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875948	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9876837	0.93[ASN][1000 genomes]
rs9877082	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880721	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883808	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9872542	PPP2R3A	cis	cerebellum	SCAN
rs9872542	MRAS	cis	parietal	SCAN
rs9872542	PPP2R3A	cis	parietal	SCAN
rs9872542	MSL2	cis	cerebellum	SCAN
rs9872542	PRR23C	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135694000-135726600	Weak transcription	Esophagus	oesophagus
2	chr3:135707000-135736400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:135707000-135741600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:135708200-135730200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:135710000-135726200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:135710000-135727200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:135710000-135737600	Weak transcription	Left Ventricle	heart
8	chr3:135710800-135727600	Weak transcription	Aorta	Aorta
9	chr3:135711600-135727800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:135711600-135731000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:135711800-135727000	Weak transcription	Pancreas	Pancrea
12	chr3:135711800-135727400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:135711800-135730400	Weak transcription	HSMM	muscle
14	chr3:135711800-135730400	Weak transcription	Osteobl	bone
15	chr3:135711800-135737600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:135712400-135721800	Weak transcription	NHDF-Ad	bronchial
17	chr3:135714000-135721200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:135714000-135729200	Weak transcription	NH-A	brain
19	chr3:135714000-135735600	Weak transcription	Fetal Heart	heart
20	chr3:135714200-135726000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:135714200-135737600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:135714600-135726000	Weak transcription	Placenta	Placenta
23	chr3:135714800-135737600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:135715000-135727000	Weak transcription	NHLF	lung
25	chr3:135715600-135732200	Weak transcription	Fetal Lung	lung
26	chr3:135715600-135737000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:135715600-135737600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:135716200-135736400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:135717000-135726200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:135717000-135726600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:135717000-135727000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:135717000-135730400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:135717200-135722200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:135717200-135725800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:135717200-135726000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:135717200-135727600	Weak transcription	Fetal Stomach	stomach
37	chr3:135717200-135737600	Weak transcription	NHEK	skin
38	chr3:135717200-135747000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:135717400-135735200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:135717800-135737400	Weak transcription	HSMMtube	muscle
41	chr3:135718000-135727200	Weak transcription	Psoas Muscle	Psoas
42	chr3:135718000-135753000	Weak transcription	Fetal Kidney	kidney
43	chr3:135718200-135736600	Weak transcription	Fetal Muscle Leg	muscle
44	chr3:135718400-135737200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:135718600-135727000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:135718800-135737600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:135719000-135730400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:135719000-135735600	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:135719000-135741600	Weak transcription	Fetal Muscle Trunk	muscle
50	chr3:135719200-135746200	Weak transcription	Fetal Intestine Large	intestine

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