Variant report

Variant	rs12403480
Chromosome Location	chr1:226005560-226005561
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226000008..226002119-chr1:226004674..226006661,2	MCF-7	breast:
2	chr1:225964451..225968253-chr1:226004384..226007160,4	K562	blood:
3	chr1:225996263..225999191-chr1:226003429..226005818,2	MCF-7	breast:
4	chr1:225965233..225968253-chr1:226004557..226007160,3	K562	blood:
5	chr1:225965293..225968073-chr1:226004323..226008130,4	MCF-7	breast:
6	chr1:226004168..226006685-chr1:226076298..226078625,2	K562	blood:
7	chr1:226004025..226006566-chr1:226007208..226010297,4	MCF-7	breast:
8	chr1:226004660..226006754-chr1:226008430..226011315,2	K562	blood:
9	chr1:226004285..226007407-chr1:226008778..226014958,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000243709	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000143819	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10753408	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10753410	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10799326	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10915881	0.88[ASN][1000 genomes]
rs41467050	0.84[ASN][1000 genomes]
rs71646748	0.81[ASN][1000 genomes]
rs71646749	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv947519	chr1:225998770-226034631	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225998400-226007800	Enhancers	Spleen	Spleen
2	chr1:225998600-226005600	Enhancers	Stomach Mucosa	stomach
3	chr1:225999200-226006400	Enhancers	Lung	lung
4	chr1:225999200-226006600	Enhancers	Psoas Muscle	Psoas
5	chr1:225999400-226006600	Enhancers	Right Ventricle	heart
6	chr1:225999400-226007800	Enhancers	Left Ventricle	heart
7	chr1:225999600-226006400	Enhancers	Brain Cingulate Gyrus	brain
8	chr1:225999800-226006400	Enhancers	Brain Hippocampus Middle	brain
9	chr1:226000000-226006600	Enhancers	Brain Substantia Nigra	brain
10	chr1:226000000-226019400	Weak transcription	Fetal Brain Female	brain
11	chr1:226000200-226006400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:226000400-226007400	Enhancers	Brain Anterior Caudate	brain
13	chr1:226000400-226015800	Enhancers	Ovary	ovary
14	chr1:226001800-226006800	Enhancers	Rectal Smooth Muscle	rectum
15	chr1:226001800-226010200	Enhancers	HepG2	liver
16	chr1:226001800-226019200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:226002600-226006400	Enhancers	Fetal Muscle Leg	muscle
18	chr1:226003200-226006400	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr1:226003200-226007600	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr1:226003400-226006000	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr1:226003400-226006200	Enhancers	Fetal Muscle Trunk	muscle
22	chr1:226003400-226006400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr1:226003400-226006400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr1:226003400-226006400	Enhancers	Gastric	stomach
25	chr1:226003400-226006600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr1:226003600-226006400	Enhancers	Duodenum Mucosa	Duodenum
27	chr1:226003800-226008800	Enhancers	Fetal Stomach	stomach
28	chr1:226004000-226005800	Enhancers	Fetal Brain Male	brain
29	chr1:226004000-226006200	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr1:226004000-226006200	Enhancers	HSMMtube	muscle
31	chr1:226004000-226006200	Enhancers	NHDF-Ad	bronchial
32	chr1:226004000-226006400	Enhancers	H1 Cell Line	embryonic stem cell
33	chr1:226004000-226006400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:226004000-226006400	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr1:226004000-226007600	Enhancers	Pancreas	Pancrea
36	chr1:226004200-226005800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:226004200-226005800	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr1:226004200-226005800	Genic enhancers	Fetal Intestine Small	intestine
39	chr1:226004200-226005800	Enhancers	Placenta	Placenta
40	chr1:226004200-226005800	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr1:226004200-226005800	Enhancers	NHLF	lung
42	chr1:226004200-226006000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:226004200-226006200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:226004200-226006400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:226004200-226006400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:226004200-226006400	Enhancers	Esophagus	oesophagus
47	chr1:226004200-226006400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr1:226004200-226006600	Enhancers	Brain Angular Gyrus	brain
49	chr1:226004400-226005600	Enhancers	Fetal Intestine Large	intestine
50	chr1:226004400-226005800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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