Variant report

Variant	rs10458379
Chromosome Location	chr1:227325273-227325274
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227314587..227318154-chr1:227324311..227326852,3	MCF-7	breast:
2	chr1:227323669..227325656-chr1:227329676..227331291,2	K562	blood:
3	chr1:227316215..227319084-chr1:227324943..227327660,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10916098	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916110	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10916117	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12035190	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12035998	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12038272	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12080452	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12095674	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12097121	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1929859	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2104863	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2458523	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2482453	0.89[ASN][1000 genomes]
rs2777833	0.86[JPT][hapmap]
rs2777841	0.82[JPT][hapmap]
rs2997438	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4551562	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4653788	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4653790	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs477373	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs482032	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs533134	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs567467	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58442036	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs595155	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61834563	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61834564	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61836477	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs645081	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6664803	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs688718	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7536444	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs871210	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv468227	chr1:227223736-227340790	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv549269	chr1:227223736-227340790	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv873240	chr1:227228946-227361072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv873241	chr1:227242247-227361072	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv549270	chr1:227290139-227361072	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
2	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
3	chr1:227272800-227331000	Weak transcription	Lung	lung
4	chr1:227286400-227328200	Weak transcription	Brain Germinal Matrix	brain
5	chr1:227287400-227360800	Weak transcription	Psoas Muscle	Psoas
6	chr1:227288000-227326400	Weak transcription	A549	lung
7	chr1:227288200-227332400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:227288400-227343000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:227288600-227328200	Weak transcription	Fetal Stomach	stomach
11	chr1:227288600-227332400	Weak transcription	NHLF	lung
12	chr1:227288600-227333600	Weak transcription	Esophagus	oesophagus
13	chr1:227288800-227330000	Weak transcription	NHDF-Ad	bronchial
14	chr1:227295200-227346400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:227296400-227326200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:227296600-227326200	Weak transcription	Fetal Lung	lung
17	chr1:227298600-227351800	Weak transcription	Hela-S3	cervix
18	chr1:227299800-227332600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:227300000-227325800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:227300000-227326400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:227300000-227328600	Weak transcription	Fetal Brain Female	brain
22	chr1:227300000-227329200	Weak transcription	Aorta	Aorta
23	chr1:227300000-227333800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:227300200-227326200	Weak transcription	Liver	Liver
26	chr1:227300200-227326400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:227300200-227334400	Weak transcription	Stomach Mucosa	stomach
28	chr1:227300600-227326600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:227307000-227326400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:227311000-227329200	Weak transcription	Pancreas	Pancrea
31	chr1:227311000-227329400	Weak transcription	Fetal Intestine Small	intestine
32	chr1:227313000-227326400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:227313600-227325600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:227314000-227326800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:227314000-227327800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:227314200-227326200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:227314200-227326400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:227314200-227327800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:227314200-227327800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:227314200-227329400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:227316000-227326200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:227316200-227326600	Weak transcription	NH-A	brain
43	chr1:227316600-227325600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:227316600-227352200	Weak transcription	Gastric	stomach
45	chr1:227316800-227325400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:227316800-227325400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:227316800-227325400	Weak transcription	Adipose Nuclei	Adipose
48	chr1:227316800-227325600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:227316800-227326000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:227316800-227326400	Weak transcription	Brain Hippocampus Middle	brain

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