Variant report

Variant	rs1464135
Chromosome Location	chr2:190042909-190042910
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	chr2:190041672..190043788-chr2:190044467..190046580,2	MCF-7	breast:
2	chr2:190036925..190039844-chr2:190040601..190043479,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204262	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10165127	0.89[EUR][1000 genomes]
rs10165257	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1016622	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10166385	0.93[ASN][1000 genomes]
rs10167242	0.82[ASN][1000 genomes]
rs10172607	0.92[ASN][1000 genomes]
rs10173224	0.94[ASN][1000 genomes]
rs10184895	0.92[ASN][1000 genomes]
rs10755002	0.92[ASN][1000 genomes]
rs10931401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10931403	0.92[ASN][1000 genomes]
rs10931405	0.86[ASN][1000 genomes]
rs10931411	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11901914	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12105389	0.81[JPT][hapmap]
rs12474942	0.94[ASN][1000 genomes]
rs12618316	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12621657	0.83[ASN][1000 genomes]
rs12999125	0.91[ASN][1000 genomes]
rs13005714	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13005834	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13006065	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13013089	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13015183	0.91[ASN][1000 genomes]
rs13019651	0.90[AFR][1000 genomes]
rs13020999	1.00[CEU][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13024858	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13028226	0.92[ASN][1000 genomes]
rs13030984	1.00[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13408928	0.94[ASN][1000 genomes]
rs13411992	0.93[ASN][1000 genomes]
rs13413518	0.94[ASN][1000 genomes]
rs1356161	0.90[ASN][1000 genomes]
rs1356164	0.84[YRI][hapmap]
rs1356166	0.91[ASN][1000 genomes]
rs1399991	0.81[JPT][hapmap]
rs1474000	0.83[ASN][1000 genomes]
rs1515864	1.00[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1515866	0.92[ASN][1000 genomes]
rs1515869	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1533618	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1546617	0.92[ASN][1000 genomes]
rs1913892	0.90[ASN][1000 genomes]
rs1949327	1.00[CEU][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1965422	0.83[YRI][hapmap]
rs1973666	0.88[ASN][1000 genomes]
rs1983318	0.91[ASN][1000 genomes]
rs2138373	1.00[CEU][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2138374	0.80[YRI][hapmap]
rs2351631	0.92[ASN][1000 genomes]
rs2351632	0.93[ASN][1000 genomes]
rs2351633	0.93[ASN][1000 genomes]
rs2351635	0.84[ASN][1000 genomes]
rs36019389	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4417749	1.00[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4667263	0.89[EUR][1000 genomes]
rs4667265	0.80[YRI][hapmap]
rs4667266	1.00[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4667268	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4667270	0.94[ASN][1000 genomes]
rs4667271	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4667275	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4998559	0.84[YRI][hapmap]
rs62182417	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6434324	1.00[CEU][hapmap];0.97[YRI][hapmap];0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6434325	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6434334	0.85[ASN][1000 genomes]
rs6434337	0.86[ASN][1000 genomes]
rs6704568	0.84[ASN][1000 genomes]
rs6708419	0.80[YRI][hapmap]
rs6728877	0.91[ASN][1000 genomes]
rs6732534	0.89[ASN][1000 genomes]
rs6741804	0.89[EUR][1000 genomes]
rs6749559	1.00[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6752781	1.00[CEU][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes]
rs6761868	0.84[ASN][1000 genomes]
rs7560973	1.00[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7561002	0.80[YRI][hapmap]
rs7574281	0.85[ASN][1000 genomes]
rs7593860	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7599222	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7603704	0.91[ASN][1000 genomes]
rs7606337	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9288163	1.00[CEU][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes]
rs939158	0.84[ASN][1000 genomes]
rs939160	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1464135	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190029600-190043400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:190029800-190043200	Weak transcription	Psoas Muscle	Psoas
3	chr2:190030400-190043400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:190034000-190043400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:190039800-190044800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:190040200-190044800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:190040400-190045000	Active TSS	Rectal Smooth Muscle	rectum
8	chr2:190040400-190045200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:190040600-190044800	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr2:190040600-190045200	Active TSS	Fetal Muscle Leg	muscle
11	chr2:190040800-190044800	Active TSS	NH-A	brain
12	chr2:190040800-190045000	Active TSS	Fetal Muscle Trunk	muscle
13	chr2:190040800-190045000	Active TSS	Right Atrium	heart
14	chr2:190040800-190045200	Active TSS	Aorta	Aorta
15	chr2:190040800-190045200	Active TSS	NHLF	lung
16	chr2:190041000-190044800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:190041000-190044800	Active TSS	Duodenum Mucosa	Duodenum
18	chr2:190041000-190045000	Active TSS	Fetal Kidney	kidney
19	chr2:190041000-190045000	Active TSS	HSMMtube	muscle
20	chr2:190041200-190044000	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr2:190041200-190044200	Active TSS	Fetal Intestine Small	intestine
22	chr2:190041200-190044800	Active TSS	Muscle Satellite Cultured Cells	--
23	chr2:190041200-190045000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:190041200-190045400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:190041200-190045400	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr2:190041400-190044800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:190041400-190044800	Active TSS	Colon Smooth Muscle	Colon
28	chr2:190041400-190045000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:190041400-190045000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:190041400-190045000	Active TSS	Adipose Nuclei	Adipose
31	chr2:190041400-190045000	Active TSS	Fetal Lung	lung
32	chr2:190041400-190045000	Active TSS	NHDF-Ad	bronchial
33	chr2:190041400-190045200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:190041400-190045200	Active TSS	Fetal Stomach	stomach
35	chr2:190041600-190043600	Weak transcription	Fetal Heart	heart
36	chr2:190041600-190044200	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr2:190041600-190044200	Active TSS	Fetal Intestine Large	intestine
38	chr2:190041600-190044800	Active TSS	Osteobl	bone
39	chr2:190041600-190045000	Active TSS	Ovary	ovary
40	chr2:190041600-190045000	Active TSS	A549	lung
41	chr2:190041600-190045200	Active TSS	Stomach Smooth Muscle	stomach
42	chr2:190041800-190044600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:190042000-190044000	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr2:190042000-190044400	Active TSS	HMEC	breast
45	chr2:190042200-190043000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:190042200-190044400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:190042200-190044400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:190042200-190044600	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr2:190042200-190044600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:190042200-190044800	Active TSS	HSMM	muscle

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