Variant report

Variant	rs12746316
Chromosome Location	chr1:227487394-227487395
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227482589..227485572-chr1:227485987..227487557,2	K562	blood:
2	chr1:227477234..227482232-chr1:227484947..227488828,5	K562	blood:
3	chr1:227480441..227495625-chr1:227496855..227507828,32	K562	blood:
4	chr1:227486106..227489054-chr1:227504943..227506984,3	K562	blood:
5	chr1:227460250..227462821-chr1:227486670..227489514,2	K562	blood:
6	chr1:227457997..227462821-chr1:227486670..227490328,4	K562	blood:
7	chr1:227485938..227488164-chr1:227505473..227507925,2	MCF-7	breast:
8	chr1:227487011..227489287-chr1:227501111..227503917,2	MCF-7	breast:
9	chr1:227486302..227488328-chr1:227502025..227504666,2	K562	blood:
10	chr1:227483357..227485572-chr1:227486057..227488627,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10916112	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10916113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10916116	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10916125	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11576239	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11584325	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11585910	1.00[AMR][1000 genomes]
rs12119153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12123597	0.85[AMR][1000 genomes]
rs12128174	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12131061	0.92[AMR][1000 genomes]
rs12131459	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12131913	0.84[CEU][hapmap]
rs12131933	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133230	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12133633	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12138092	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12138364	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12138383	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12138664	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12144205	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12751015	0.85[CEU][hapmap]
rs12754677	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12755770	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1513607	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1513613	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17545704	0.83[CEU][hapmap]
rs17613235	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2063661	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28648445	1.00[AMR][1000 genomes]
rs34113967	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34702208	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34897490	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35160496	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35952573	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4308948	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs61834323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834324	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834326	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834590	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61834625	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61834626	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6660168	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6675408	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6675572	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6678714	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6697583	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512871	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs7518813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539662	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7543419	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7548118	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[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	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	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
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227462600-227500200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:227469200-227500200	Weak transcription	Left Ventricle	heart
3	chr1:227469200-227502600	Weak transcription	HSMM	muscle
4	chr1:227469600-227501800	Weak transcription	Fetal Stomach	stomach
5	chr1:227475000-227491800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:227475000-227502000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:227475200-227500200	Weak transcription	Fetal Intestine Small	intestine
8	chr1:227478000-227491800	Weak transcription	Psoas Muscle	Psoas
9	chr1:227483600-227489800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:227483600-227500200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:227483800-227500400	Weak transcription	Right Atrium	heart
12	chr1:227485600-227491200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:227485800-227488000	Enhancers	Hela-S3	cervix
14	chr1:227486000-227488000	Enhancers	Colon Smooth Muscle	Colon
15	chr1:227486200-227487400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr1:227486200-227487600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:227486200-227487800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:227486200-227487800	Enhancers	Liver	Liver
19	chr1:227486200-227488600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:227486400-227488000	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:227486400-227488800	Enhancers	Stomach Mucosa	stomach
22	chr1:227486600-227487600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:227486600-227487800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr1:227486600-227487800	Flanking Active TSS	HUVEC	blood vessel
25	chr1:227486600-227488000	Active TSS	K562	blood
26	chr1:227486600-227491200	Weak transcription	Aorta	Aorta
27	chr1:227486600-227494000	Weak transcription	Brain Substantia Nigra	brain
28	chr1:227486600-227494000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:227486600-227497800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:227486800-227487600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:227486800-227487600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:227487000-227487400	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr1:227487000-227487600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:227487000-227487600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:227487000-227487600	Enhancers	HSMMtube	muscle
36	chr1:227487000-227487600	Enhancers	Osteobl	bone
37	chr1:227487000-227487800	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr1:227487000-227487800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:227487000-227487800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr1:227487000-227487800	Enhancers	Adipose Nuclei	Adipose
41	chr1:227487000-227487800	Enhancers	Fetal Lung	lung
42	chr1:227487000-227487800	Enhancers	NHDF-Ad	bronchial
43	chr1:227487000-227487800	Enhancers	NHLF	lung
44	chr1:227487000-227488000	Enhancers	Brain Anterior Caudate	brain
45	chr1:227487000-227488000	Enhancers	NHEK	skin
46	chr1:227487000-227495800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:227487000-227496000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:227487000-227496200	Weak transcription	Fetal Heart	heart
49	chr1:227487000-227500200	Weak transcription	HMEC	breast
50	chr1:227487000-227501800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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