Variant report

Variant	rs12028523
Chromosome Location	chr1:227544707-227544708
allele	C/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	chr1:227500332..227503244-chr1:227542452..227546426,3	K562	blood:
2	chr1:227538699..227541484-chr1:227541523..227544732,3	K562	blood:
3	chr1:227530004..227531829-chr1:227543637..227545711,2	K562	blood:
4	chr1:227504395..227506976-chr1:227543254..227545122,2	MCF-7	breast:
5	chr1:227544242..227546740-chr1:227566888..227569637,2	K562	blood:
6	chr1:227530329..227533212-chr1:227543637..227546131,2	K562	blood:
7	chr1:227542971..227547040-chr1:227548442..227550941,4	K562	blood:
8	chr1:227503674..227505956-chr1:227543309..227545272,2	MCF-7	breast:
9	chr1:227538792..227542003-chr1:227542964..227545271,3	K562	blood:
10	chr1:227502375..227508330-chr1:227544221..227551404,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10458380	0.81[ASN][1000 genomes]
rs10753434	0.86[ASN][1000 genomes]
rs10799412	0.86[ASN][1000 genomes]
rs10916123	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916124	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916127	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916128	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916129	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10916133	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12022275	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12023427	0.96[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];0.97[ASN][1000 genomes]
rs12047964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12057466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12062358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12081061	0.81[CEU][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12085773	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16847682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847690	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654860	0.90[ASN][1000 genomes]
rs4075196	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4075861	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233226	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4294380	0.81[YRI][hapmap]
rs4531260	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653497	1.00[ASN][1000 genomes]
rs4653498	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs4653826	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4653828	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4653831	0.92[ASN][1000 genomes]
rs59718661	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61833060	1.00[ASN][1000 genomes]
rs6690898	0.96[CEU][hapmap];0.95[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]
rs67343057	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72632826	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72759365	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7519870	0.99[ASN][1000 genomes]
rs7540726	0.82[ASN][1000 genomes]
rs7540833	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7541775	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7553358	0.96[CEU][hapmap];0.96[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];0.99[ASN][1000 genomes]
rs7555764	0.87[ASN][1000 genomes]
rs7556096	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[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:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227539200-227545000	Weak transcription	Brain Substantia Nigra	brain
2	chr1:227539400-227545000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:227539600-227544800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:227542600-227547400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:227542800-227545800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr1:227543400-227545800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr1:227543600-227545000	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr1:227543600-227545800	Enhancers	H9 Cell Line	embryonic stem cell
9	chr1:227544000-227546200	Enhancers	Fetal Intestine Large	intestine
10	chr1:227544200-227544800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:227544200-227544800	Enhancers	HMEC	breast
12	chr1:227544200-227545000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr1:227544200-227545000	Enhancers	Spleen	Spleen
14	chr1:227544200-227545000	Enhancers	HSMM	muscle
15	chr1:227544200-227545000	Enhancers	Osteobl	bone
16	chr1:227544200-227545200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:227544200-227545200	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr1:227544200-227545800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:227544200-227545800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:227544200-227545800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:227544200-227545800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:227544200-227545800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:227544200-227545800	Enhancers	Adipose Nuclei	Adipose
24	chr1:227544200-227545800	Enhancers	Fetal Muscle Trunk	muscle
25	chr1:227544200-227545800	Enhancers	Fetal Muscle Leg	muscle
26	chr1:227544200-227545800	Enhancers	Placenta	Placenta
27	chr1:227544200-227545800	Enhancers	Left Ventricle	heart
28	chr1:227544200-227545800	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr1:227544200-227545800	Flanking Active TSS	A549	lung
30	chr1:227544200-227545800	Flanking Active TSS	Hela-S3	cervix
31	chr1:227544200-227545800	Flanking Active TSS	HUVEC	blood vessel
32	chr1:227544200-227545800	Enhancers	NH-A	brain
33	chr1:227544200-227546000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:227544200-227546000	Enhancers	Fetal Intestine Small	intestine
35	chr1:227544200-227546000	Enhancers	Stomach Mucosa	stomach
36	chr1:227544200-227546000	Enhancers	NHLF	lung
37	chr1:227544200-227546200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:227544200-227546400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:227544200-227546600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr1:227544200-227547600	Enhancers	Lung	lung
41	chr1:227544400-227544800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr1:227544400-227544800	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr1:227544400-227544800	Enhancers	HSMMtube	muscle
44	chr1:227544400-227545000	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr1:227544400-227545200	Enhancers	Esophagus	oesophagus
46	chr1:227544400-227545200	Enhancers	Fetal Lung	lung
47	chr1:227544400-227545600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr1:227544400-227545600	Flanking Active TSS	NHEK	skin
49	chr1:227544400-227545800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:227544400-227545800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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