Variant report

Variant	rs9843725
Chromosome Location	chr3:135702865-135702866
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	chr3:135701943..135704037-chr3:135704437..135706421,2	K562	blood:

Extended variants
information (count: 117 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10048942	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10049233	1.00[ASN][1000 genomes]
rs10512981	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs10935175	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072596	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13082684	1.00[ASN][1000 genomes]
rs13097946	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13098245	0.95[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13322891	0.92[ASN][1000 genomes]
rs13325914	0.95[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13434196	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs1356664	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1401545	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1403766	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1403767	0.92[ASN][1000 genomes]
rs1403770	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523595	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1523596	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1523597	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1568350	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16843509	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs17196987	0.87[GIH][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17197552	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17250445	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2204259	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs28449384	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28570106	0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28576629	1.00[ASN][1000 genomes]
rs28855968	0.96[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28875187	0.92[ASN][1000 genomes]
rs34311570	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34409306	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34522617	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34767379	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35257855	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35722356	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36039354	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073308	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs55678980	0.92[ASN][1000 genomes]
rs56308637	0.92[ASN][1000 genomes]
rs66544356	0.80[EUR][1000 genomes]
rs67039922	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6771224	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6771997	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6774289	1.00[CEU][hapmap];1.00[CHD][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]
rs6775778	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6786769	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6802139	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6807058	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807242	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6807565	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809006	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6810223	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71336046	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73222222	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7427833	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7433567	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621331	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7621396	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621425	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7628848	1.00[ASN][1000 genomes]
rs7638129	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs7641070	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643661	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs870812	0.92[ASN][1000 genomes]
rs908825	0.92[ASN][1000 genomes]
rs9289502	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9289503	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9808979	0.95[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9812561	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9814505	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9814557	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819440	0.92[ASN][1000 genomes]
rs9820189	0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9825239	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826806	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9829329	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9829476	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9833699	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9834104	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9834624	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9836374	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9836758	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837355	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9837855	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9839259	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9842840	0.91[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9842864	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844478	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9846137	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9848322	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849088	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs9851361	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9853577	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9854494	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9862264	0.95[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9862743	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9862763	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9862777	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864247	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9864514	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9864656	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9864775	0.80[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9868246	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9870581	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9872542	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]
rs9875328	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9875948	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]
rs9877082	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9877722	0.92[ASN][1000 genomes]
rs9880721	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9883808	0.95[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9843725	PPP2R3A	cis	cerebellum	SCAN
rs9843725	MSL2	cis	cerebellum	SCAN
rs9843725	MRAS	cis	parietal	SCAN
rs9843725	PRR23C	cis	parietal	SCAN
rs9843725	RNF184	cis	multi-tissue	Pritchard
rs9843725	PPP2R3A	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135693600-135704000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:135694000-135713600	Weak transcription	Fetal Lung	lung
3	chr3:135694000-135726600	Weak transcription	Esophagus	oesophagus
4	chr3:135694200-135707400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:135694200-135707400	Weak transcription	Gastric	stomach
6	chr3:135694200-135708800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:135694200-135709600	Weak transcription	Right Atrium	heart
8	chr3:135694200-135713400	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:135699000-135703200	Enhancers	Colon Smooth Muscle	Colon
10	chr3:135699000-135704800	Enhancers	Rectal Smooth Muscle	rectum
11	chr3:135699600-135703400	Enhancers	NHDF-Ad	bronchial
12	chr3:135699800-135703200	Enhancers	NHLF	lung
13	chr3:135699800-135709600	Weak transcription	Right Ventricle	heart
14	chr3:135700200-135704200	Weak transcription	Brain Substantia Nigra	brain
15	chr3:135700400-135703400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:135700400-135708800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:135700800-135703000	Enhancers	Osteobl	bone
18	chr3:135701000-135703200	Enhancers	A549	lung
19	chr3:135701200-135703000	Enhancers	NHEK	skin
20	chr3:135701600-135720600	Weak transcription	Ovary	ovary
21	chr3:135701800-135703000	Enhancers	Fetal Heart	heart
22	chr3:135701800-135706600	Weak transcription	Aorta	Aorta
23	chr3:135701800-135707200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:135702000-135703400	Weak transcription	Psoas Muscle	Psoas
25	chr3:135702000-135703600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:135702000-135704800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:135702000-135705200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:135702200-135703600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:135702200-135706200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:135702200-135710200	Weak transcription	HSMMtube	muscle
31	chr3:135702600-135703200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:135702600-135703400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:135702600-135704000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:135702600-135707800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:135702600-135708000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:135702600-135709800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:135702600-135710600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:135702800-135706600	Weak transcription	HMEC	breast
39	chr3:135702800-135706600	Weak transcription	NH-A	brain

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