Variant report

Variant	rs12074859
Chromosome Location	chr1:92199509-92199510
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:92195746..92200158-chr1:92212228..92214643,4	K562	blood:
2	chr1:92196960..92199922-chr1:92201744..92205146,4	K562	blood:
3	chr1:92198152..92200213-chr1:92201193..92206399,7	K562	blood:
4	chr1:92196725..92200248-chr1:92206849..92210560,4	K562	blood:
5	chr1:92197642..92200532-chr1:92350997..92352784,2	K562	blood:
6	chr1:92178299..92180371-chr1:92198181..92200886,2	K562	blood:
7	chr1:92197202..92203288-chr1:92206365..92210533,5	K562	blood:
8	chr1:92198271..92200616-chr1:92212506..92214595,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000069702	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10783003	0.81[ASN][1000 genomes]
rs10783004	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165354	0.80[ASN][1000 genomes]
rs11165372	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165376	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11165380	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11578802	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069138	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12069176	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12124904	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2306887	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4658264	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6604051	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7512284	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7517044	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv2763581	chr1:92068967-92203803	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1014990	chr1:92084142-92206674	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92173200-92202400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:92189200-92202200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:92190600-92201400	Genic enhancers	NHDF-Ad	bronchial
4	chr1:92191800-92204000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:92192600-92200600	Genic enhancers	Fetal Muscle Leg	muscle
6	chr1:92193000-92202400	Weak transcription	Aorta	Aorta
7	chr1:92193600-92200600	Strong transcription	HepG2	liver
8	chr1:92194400-92201000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:92196000-92201200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:92196400-92200200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:92196600-92199600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:92197000-92215200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:92197200-92202400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:92197200-92202600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:92197200-92215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:92197600-92203000	Enhancers	Fetal Intestine Small	intestine
17	chr1:92197600-92203400	Enhancers	Fetal Intestine Large	intestine
18	chr1:92197600-92230000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:92197800-92200600	Weak transcription	Small Intestine	intestine
20	chr1:92197800-92211000	Weak transcription	Colonic Mucosa	Colon
21	chr1:92198000-92200800	Strong transcription	Placenta	Placenta
22	chr1:92198000-92210400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:92198200-92200800	Weak transcription	Fetal Heart	heart
24	chr1:92198200-92202200	Weak transcription	Brain Anterior Caudate	brain
25	chr1:92198200-92202400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:92198200-92202400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:92198200-92202400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:92198200-92202400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:92198200-92202400	Weak transcription	Stomach Mucosa	stomach
30	chr1:92198200-92202600	Weak transcription	Brain Angular Gyrus	brain
31	chr1:92198200-92206600	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:92198200-92224400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:92198400-92199800	Weak transcription	Left Ventricle	heart
34	chr1:92198400-92200000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:92198400-92200000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:92198400-92200600	Strong transcription	Adipose Nuclei	Adipose
37	chr1:92198400-92201000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr1:92198400-92201800	Weak transcription	Psoas Muscle	Psoas
39	chr1:92198400-92202000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:92198400-92202000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:92198400-92202000	Weak transcription	HSMM	muscle
42	chr1:92198400-92202400	Weak transcription	Esophagus	oesophagus
43	chr1:92198400-92202600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:92198400-92202600	Weak transcription	Pancreas	Pancrea
45	chr1:92198400-92202600	Weak transcription	Right Atrium	heart
46	chr1:92198400-92202800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:92198400-92207000	Weak transcription	Gastric	stomach
48	chr1:92198400-92207400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:92198400-92210400	Weak transcription	HUVEC	blood vessel
50	chr1:92198600-92199600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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