Variant report

Variant	rs13097946
Chromosome Location	chr3:135713622-135713623
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135713331..135715751-chr3:135731248..135733189,2	MCF-7	breast:
2	chr3:135707339..135711075-chr3:135711449..135714009,4	MCF-7	breast:

Extended variants
information (count: 114 )
Associated
traits (count: 6 )

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];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13072596	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082684	0.84[ASN][1000 genomes]
rs13098245	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434196	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1403766	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1403770	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1523595	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523596	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523597	0.96[AMR][1000 genomes];0.95[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];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17196987	0.97[GIH][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17197552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17250445	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2204259	0.82[CEU][hapmap];0.93[ASN][1000 genomes]
rs28449384	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28576629	0.84[ASN][1000 genomes]
rs34311570	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34409306	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34522617	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34767379	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35257855	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36039354	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4073308	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[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	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771224	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.97[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[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775778	1.00[CHD][hapmap];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];0.99[AFR][1000 genomes];0.98[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];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6807242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807565	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6809006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810223	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71336046	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73222222	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7427833	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7433567	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[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[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621396	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[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];0.90[AMR][1000 genomes];0.97[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	0.86[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];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289502	0.81[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];0.90[AMR][1000 genomes];0.98[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];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813082	0.93[ASN][1000 genomes]
rs9814557	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.98[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];0.88[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];0.86[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	0.90[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836758	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9837355	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9839259	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9842840	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842864	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9843725	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]
rs9844478	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9846137	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848322	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9849088	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9851361	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853577	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[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];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862743	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9862763	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862777	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9864247	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9864514	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864656	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9864775	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs9868246	0.95[CEU][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870581	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9872542	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]
rs9875328	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875948	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9876837	0.93[ASN][1000 genomes]
rs9877082	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880721	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883808	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13097946	PRR23C	cis	parietal	SCAN
rs13097946	RNF184	cis	multi-tissue	Pritchard
rs13097946	PPP2R3A	cis	parietal	SCAN
rs13097946	MRAS	cis	parietal	SCAN
rs13097946	PPP2R3A	cis	cerebellum	SCAN
rs13097946	MSL2	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135694000-135726600	Weak transcription	Esophagus	oesophagus
2	chr3:135701600-135720600	Weak transcription	Ovary	ovary
3	chr3:135704600-135716400	Weak transcription	Brain Substantia Nigra	brain
4	chr3:135707000-135736400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:135707000-135741600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:135708200-135716600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:135708200-135730200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:135709800-135717800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:135710000-135716800	Weak transcription	Psoas Muscle	Psoas
10	chr3:135710000-135726200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:135710000-135727200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:135710000-135737600	Weak transcription	Left Ventricle	heart
13	chr3:135710600-135715400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:135710800-135713800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:135710800-135727600	Weak transcription	Aorta	Aorta
16	chr3:135711600-135713800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:135711600-135714800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:135711600-135717000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:135711600-135727800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:135711600-135731000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:135711800-135714600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:135711800-135727000	Weak transcription	Pancreas	Pancrea
23	chr3:135711800-135727400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:135711800-135730400	Weak transcription	HSMM	muscle
25	chr3:135711800-135730400	Weak transcription	Osteobl	bone
26	chr3:135711800-135737600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:135712400-135721800	Weak transcription	NHDF-Ad	bronchial
28	chr3:135713000-135714200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:135713000-135714200	Enhancers	NHEK	skin
30	chr3:135713200-135713800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:135713200-135714000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:135713200-135714000	Enhancers	Fetal Heart	heart
33	chr3:135713200-135714200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:135713200-135714200	Enhancers	NHLF	lung
35	chr3:135713200-135714400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:135713400-135714000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:135713400-135714000	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:135713400-135714000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:135713400-135714000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:135713400-135714000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:135713400-135714000	Enhancers	Brain Hippocampus Middle	brain
42	chr3:135713400-135714000	Enhancers	Colon Smooth Muscle	Colon
43	chr3:135713400-135714000	Enhancers	K562	blood
44	chr3:135713600-135713800	Enhancers	H1 Cell Line	embryonic stem cell
45	chr3:135713600-135713800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:135713600-135713800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:135713600-135713800	Enhancers	Fetal Lung	lung
48	chr3:135713600-135714000	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr3:135713600-135714000	Enhancers	Brain Germinal Matrix	brain
50	chr3:135713600-135714000	Enhancers	NH-A	brain

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