Variant report

Variant	rs3845419
Chromosome Location	chr1:180899683-180899684
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180893452..180895106-chr1:180898363..180900238,2	K562	blood:
2	chr1:180898990..180902817-chr1:180903024..180908375,8	MCF-7	breast:
3	chr1:180892623..180894701-chr1:180898056..180900567,2	MCF-7	breast:
4	chr1:180893606..180898291-chr1:180898738..180903047,8	K562	blood:

Variant related genes	Relation type
ENSG00000135835	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10914137	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10914139	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3845418	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60757611	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530232	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv872579	chr1:180881148-180931508	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1001918	chr1:180886750-180908005	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180886000-180911000	Enhancers	Fetal Thymus	thymus
2	chr1:180887600-180915800	Weak transcription	Osteobl	bone
3	chr1:180888600-180917200	Weak transcription	Gastric	stomach
4	chr1:180891600-180901000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr1:180895200-180902200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:180895400-180900800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:180895400-180914200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:180896000-180902600	Enhancers	Thymus	Thymus
9	chr1:180896200-180903600	Weak transcription	Primary B cells from cord blood	blood
10	chr1:180896200-180903600	Weak transcription	GM12878-XiMat	blood
11	chr1:180896200-180908600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:180896400-180905800	Weak transcription	NHDF-Ad	bronchial
13	chr1:180896400-180915400	Weak transcription	HSMMtube	muscle
14	chr1:180896400-180917400	Weak transcription	Fetal Kidney	kidney
15	chr1:180896600-180902400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:180896600-180904000	Weak transcription	NHLF	lung
17	chr1:180896600-180904400	Weak transcription	Colonic Mucosa	Colon
18	chr1:180896600-180913400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:180896800-180900800	Weak transcription	K562	blood
20	chr1:180896800-180904400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:180896800-180921800	Weak transcription	Pancreas	Pancrea
22	chr1:180897000-180904200	Weak transcription	Fetal Intestine Large	intestine
23	chr1:180897400-180902200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:180897400-180915400	Weak transcription	HSMM	muscle
25	chr1:180897600-180900000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:180897600-180900200	Strong transcription	Aorta	Aorta
27	chr1:180897800-180900600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:180897800-180900800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:180897800-180902000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:180897800-180902000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:180897800-180902000	Genic enhancers	Fetal Muscle Leg	muscle
32	chr1:180897800-180902400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:180898000-180900200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:180898000-180900400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:180898000-180901000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:180898000-180904400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:180898000-180904400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:180898200-180899800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:180898200-180901200	Enhancers	Fetal Brain Male	brain
40	chr1:180898200-180901200	Genic enhancers	Fetal Muscle Trunk	muscle
41	chr1:180898200-180902200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:180898200-180904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:180898200-180905000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:180898400-180901200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:180898400-180904600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr1:180898400-180910600	Weak transcription	Brain Substantia Nigra	brain
47	chr1:180898600-180903400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr1:180898800-180902400	Weak transcription	Fetal Heart	heart
49	chr1:180899000-180899800	Weak transcription	Fetal Brain Female	brain
50	chr1:180899000-180900000	Weak transcription	Brain Germinal Matrix	brain

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