Variant report

Variant	rs41478946
Chromosome Location	chr2:46940505-46940506
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46930002..46931505-chr2:46938996..46941968,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10495938	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11889273	0.91[AFR][1000 genomes]
rs11892177	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11892710	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11893159	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11893443	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11893955	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11901688	0.88[ASN][1000 genomes]
rs17035540	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17771005	0.86[AFR][1000 genomes]
rs17771237	0.84[AFR][1000 genomes]
rs17771255	0.84[AFR][1000 genomes]
rs17771357	0.82[AFR][1000 genomes]
rs17772309	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17821941	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17822668	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17822704	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41320947	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs41349351	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41363351	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41370847	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41375646	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs41379147	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs41432848	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4575769	0.89[AFR][1000 genomes]
rs62134765	0.93[AFR][1000 genomes]
rs6721999	1.00[ASN][1000 genomes]
rs6731970	0.86[AFR][1000 genomes]
rs6749450	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72802460	0.87[AFR][1000 genomes]
rs7591613	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7606134	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9677272	0.91[AFR][1000 genomes]
rs9677705	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
6	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46928000-46943600	Weak transcription	Thymus	Thymus
2	chr2:46928600-46944400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:46928800-46946200	Weak transcription	NHEK	skin
4	chr2:46932600-46944200	Weak transcription	Aorta	Aorta
5	chr2:46933000-46943600	Weak transcription	Left Ventricle	heart
6	chr2:46934000-46944200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:46934000-46947800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:46934400-46943600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:46934600-46946400	Weak transcription	HSMM	muscle
10	chr2:46935200-46944000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:46936000-46941400	Weak transcription	Liver	Liver
12	chr2:46936000-46945000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:46936400-46942200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:46936400-46943600	Weak transcription	Pancreas	Pancrea
15	chr2:46936600-46943600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:46936800-46942800	Weak transcription	NH-A	brain
17	chr2:46936800-46946200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:46937000-46943800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:46937000-46944000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:46937000-46944200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:46937600-46943600	Weak transcription	Ovary	ovary
22	chr2:46938600-46941200	Weak transcription	Osteobl	bone
23	chr2:46938600-46942600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:46938600-46943600	Weak transcription	NHLF	lung
25	chr2:46939000-46940600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:46939000-46944000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:46940000-46943800	Weak transcription	NHDF-Ad	bronchial
28	chr2:46940200-46940600	ZNF genes & repeats	Fetal Stomach	stomach
29	chr2:46940200-46940600	Enhancers	Psoas Muscle	Psoas
30	chr2:46940200-46941000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:46940200-46941200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr2:46940400-46944000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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