Variant report

Variant	rs6775778
Chromosome Location	chr3:135726679-135726680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10048942	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10049233	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512981	1.00[JPT][hapmap]
rs10512990	0.94[CEU][hapmap]
rs10935175	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs12330335	0.95[CEU][hapmap]
rs13068210	0.93[CEU][hapmap]
rs13072596	0.84[ASN][1000 genomes]
rs13079205	0.95[CEU][hapmap];0.84[MEX][hapmap]
rs13081671	0.95[CEU][hapmap];0.83[MEX][hapmap]
rs13082684	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097248	0.88[CEU][hapmap]
rs13097946	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs13098245	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13322891	0.92[ASN][1000 genomes]
rs13325914	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13434196	1.00[JPT][hapmap]
rs1356664	0.92[ASN][1000 genomes]
rs1393786	0.95[CEU][hapmap];0.84[MEX][hapmap]
rs1393787	0.95[CEU][hapmap];0.84[MEX][hapmap]
rs1401545	0.92[ASN][1000 genomes]
rs1403763	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs1403766	0.92[ASN][1000 genomes]
rs1403767	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1403770	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs1523595	0.84[ASN][1000 genomes]
rs1523596	0.84[ASN][1000 genomes]
rs1523597	0.84[ASN][1000 genomes]
rs1568350	0.92[ASN][1000 genomes]
rs16843509	1.00[JPT][hapmap]
rs17196987	0.84[ASN][1000 genomes]
rs17197552	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs28449384	1.00[ASN][1000 genomes]
rs28509770	0.80[EUR][1000 genomes]
rs28535121	0.95[CEU][hapmap];0.84[MEX][hapmap]
rs28570106	0.92[ASN][1000 genomes]
rs28576629	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28855968	0.92[ASN][1000 genomes]
rs28875187	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34522617	1.00[ASN][1000 genomes]
rs34767379	1.00[ASN][1000 genomes]
rs35352346	0.89[CEU][hapmap]
rs35722356	0.92[ASN][1000 genomes]
rs36039354	1.00[ASN][1000 genomes]
rs4073308	0.84[ASN][1000 genomes]
rs4718	0.92[ASN][1000 genomes]
rs55678980	0.92[ASN][1000 genomes]
rs56308637	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6439629	0.95[CEU][hapmap]
rs67039922	0.84[ASN][1000 genomes]
rs6767060	0.95[CEU][hapmap]
rs6769762	0.84[CEU][hapmap];0.84[MEX][hapmap]
rs6771224	0.84[ASN][1000 genomes]
rs6771997	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6774289	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs6786582	0.95[CEU][hapmap];0.84[MEX][hapmap]
rs6786769	0.84[ASN][1000 genomes]
rs6792630	0.94[CEU][hapmap]
rs6793835	0.95[CEU][hapmap];0.84[MEX][hapmap]
rs6799056	0.89[CEU][hapmap]
rs6799320	0.84[CEU][hapmap]
rs6799517	0.80[EUR][1000 genomes]
rs6802139	1.00[JPT][hapmap]
rs6807058	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6807242	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6807565	1.00[ASN][1000 genomes]
rs6809006	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs6810223	0.84[ASN][1000 genomes]
rs73222222	1.00[ASN][1000 genomes]
rs7427833	1.00[ASN][1000 genomes]
rs7433567	1.00[ASN][1000 genomes]
rs7621331	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs7621396	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs7621425	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7628848	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638129	1.00[JPT][hapmap]
rs7641070	1.00[ASN][1000 genomes]
rs7643661	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs870812	0.92[ASN][1000 genomes]
rs908825	0.92[ASN][1000 genomes]
rs9289502	0.84[ASN][1000 genomes]
rs9289503	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9653930	0.95[CEU][hapmap]
rs9808979	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9812561	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9814505	0.92[ASN][1000 genomes]
rs9814557	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9819440	0.92[ASN][1000 genomes]
rs9820189	0.92[ASN][1000 genomes]
rs9825239	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9826806	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9827662	0.95[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9829329	1.00[JPT][hapmap]
rs9829476	1.00[JPT][hapmap]
rs9833699	0.92[ASN][1000 genomes]
rs9834104	0.84[ASN][1000 genomes]
rs9834624	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs9836374	1.00[JPT][hapmap]
rs9836758	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9837355	0.84[ASN][1000 genomes]
rs9837855	0.92[ASN][1000 genomes]
rs9839259	1.00[JPT][hapmap]
rs9842840	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9842864	1.00[ASN][1000 genomes]
rs9843725	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9844478	1.00[JPT][hapmap]
rs9846137	0.84[ASN][1000 genomes]
rs9848322	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9848926	0.95[CEU][hapmap];0.84[MEX][hapmap]
rs9849088	1.00[JPT][hapmap]
rs9851361	0.84[ASN][1000 genomes]
rs9852406	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9853577	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9854494	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs9862264	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9862763	0.84[ASN][1000 genomes]
rs9862777	1.00[ASN][1000 genomes]
rs9864247	1.00[JPT][hapmap]
rs9864514	0.84[ASN][1000 genomes]
rs9864656	1.00[JPT][hapmap]
rs9864775	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9868246	0.84[ASN][1000 genomes]
rs9870581	1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs9872542	1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs9875328	0.84[ASN][1000 genomes]
rs9875948	1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs9877082	0.84[ASN][1000 genomes]
rs9877722	0.92[ASN][1000 genomes]
rs9880721	0.84[ASN][1000 genomes]
rs9881400	0.95[CEU][hapmap];0.84[MEX][hapmap]
rs9883808	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6775778	MRAS	cis	parietal	SCAN
rs6775778	RNF184	cis	multi-tissue	Pritchard
rs6775778	PPP2R3A	cis	cerebellum	SCAN
rs6775778	MSL2	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135707000-135736400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr3:135707000-135741600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:135708200-135730200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:135710000-135727200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:135710000-135737600	Weak transcription	Left Ventricle	heart
6	chr3:135710800-135727600	Weak transcription	Aorta	Aorta
7	chr3:135711600-135727800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:135711600-135731000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:135711800-135727000	Weak transcription	Pancreas	Pancrea
10	chr3:135711800-135727400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:135711800-135730400	Weak transcription	HSMM	muscle
12	chr3:135711800-135730400	Weak transcription	Osteobl	bone
13	chr3:135711800-135737600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:135714000-135729200	Weak transcription	NH-A	brain
15	chr3:135714000-135735600	Weak transcription	Fetal Heart	heart
16	chr3:135714200-135737600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:135714800-135737600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:135715000-135727000	Weak transcription	NHLF	lung
19	chr3:135715600-135732200	Weak transcription	Fetal Lung	lung
20	chr3:135715600-135737000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:135715600-135737600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:135716200-135736400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:135717000-135727000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:135717000-135730400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:135717200-135727600	Weak transcription	Fetal Stomach	stomach
26	chr3:135717200-135737600	Weak transcription	NHEK	skin
27	chr3:135717200-135747000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:135717400-135735200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:135717800-135737400	Weak transcription	HSMMtube	muscle
30	chr3:135718000-135727200	Weak transcription	Psoas Muscle	Psoas
31	chr3:135718000-135753000	Weak transcription	Fetal Kidney	kidney
32	chr3:135718200-135736600	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:135718400-135737200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:135718600-135727000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:135718800-135737600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:135719000-135730400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:135719000-135735600	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:135719000-135741600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:135719200-135746200	Weak transcription	Fetal Intestine Large	intestine
40	chr3:135721000-135727600	Weak transcription	Ovary	ovary
41	chr3:135721800-135763600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:135722800-135727200	Weak transcription	NHDF-Ad	bronchial
43	chr3:135723600-135727000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:135724000-135727000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:135725400-135727800	Enhancers	Placenta Amnion	Placenta Amnion
46	chr3:135725800-135727800	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr3:135726000-135727400	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr3:135726000-135727400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:135726000-135728000	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr3:135726200-135727800	Enhancers	H1 Cell Line	embryonic stem cell

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