Variant report

Variant	rs41464348
Chromosome Location	chr2:33527299-33527300
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	chr2:33514697..33516578-chr2:33527291..33531093,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000049323	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10208199	0.88[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs11124311	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11124312	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11124313	0.88[MEX][hapmap]
rs13392154	0.83[MEX][hapmap]
rs3754829	0.92[CEU][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3769542	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs3769544	0.80[ASN][1000 genomes]
rs3820911	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4670387	0.88[MEX][hapmap]
rs4670408	0.83[MEX][hapmap]
rs6543704	0.88[MEX][hapmap]
rs6543705	0.88[MEX][hapmap]
rs6735659	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6739506	0.84[MEX][hapmap]
rs6740415	0.88[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];0.87[TSI][hapmap]
rs6740443	0.88[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];0.85[TSI][hapmap]
rs6740448	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs723043	0.88[MEX][hapmap]
rs749455	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7575377	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579452	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7595330	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs817534	0.88[MEX][hapmap]
rs817535	0.85[CEU][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs817536	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs817537	0.88[MEX][hapmap];0.81[TSI][hapmap]
rs877672	0.92[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs935996	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9678322	0.88[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	nsv873791	chr2:33489975-33586776	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv1011020	chr2:33508811-33527784	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2754325	chr2:33524956-33527587	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	19893584	GWAS catalog

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33492400-33547400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:33501200-33528800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:33502600-33537000	Weak transcription	Fetal Intestine Large	intestine
4	chr2:33507000-33528600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:33517000-33528800	Weak transcription	Psoas Muscle	Psoas
6	chr2:33517000-33529200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:33517000-33529400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:33517000-33529600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:33517200-33533000	Weak transcription	Brain Substantia Nigra	brain
10	chr2:33517200-33533200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:33517200-33537400	Weak transcription	Fetal Brain Male	brain
12	chr2:33517200-33545000	Weak transcription	Fetal Kidney	kidney
13	chr2:33517200-33545800	Weak transcription	Fetal Lung	lung
14	chr2:33517200-33546400	Weak transcription	Brain Angular Gyrus	brain
15	chr2:33517600-33532600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:33517600-33532800	Weak transcription	Brain Anterior Caudate	brain
17	chr2:33517800-33543400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:33523200-33529400	Weak transcription	HUVEC	blood vessel
19	chr2:33523400-33528800	Weak transcription	Ovary	ovary
20	chr2:33523400-33532600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:33523400-33545200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:33523600-33528800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:33523600-33529400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:33523600-33529400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:33523600-33546200	Weak transcription	K562	blood
26	chr2:33523800-33529000	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:33523800-33536400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:33523800-33550600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:33524200-33529400	Weak transcription	HSMMtube	muscle
30	chr2:33524200-33546600	Weak transcription	Small Intestine	intestine
31	chr2:33524400-33527400	Strong transcription	NHDF-Ad	bronchial
32	chr2:33524600-33530000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:33524600-33531600	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr2:33524600-33535800	Strong transcription	Osteobl	bone
35	chr2:33524600-33537600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:33524800-33533400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:33525000-33537600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:33525200-33530000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:33525400-33527400	Strong transcription	Right Ventricle	heart
40	chr2:33525400-33527600	Strong transcription	Left Ventricle	heart
41	chr2:33525400-33528400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:33525400-33531000	Strong transcription	NHLF	lung
43	chr2:33525800-33527600	Strong transcription	Liver	Liver
44	chr2:33525800-33531000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:33526200-33527800	Strong transcription	Placenta	Placenta
46	chr2:33526400-33527800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr2:33526600-33527800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:33526600-33528800	Strong transcription	Fetal Stomach	stomach
49	chr2:33526800-33527800	Strong transcription	Fetal Heart	heart
50	chr2:33526800-33528800	Strong transcription	Aorta	Aorta

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