Variant report

Variant	rs12619401
Chromosome Location	chr2:179327978-179327979
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179325016..179328515-chr2:179328760..179332475,4	MCF-7	breast:
2	chr2:179314249..179317479-chr2:179327619..179332634,7	K562	blood:

Variant related genes	Relation type
ENSG00000204311	Chromatin interaction
ENSG00000180228	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10497515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10497516	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12612917	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12613131	0.83[AMR][1000 genomes]
rs12613303	1.00[AMR][1000 genomes]
rs12615980	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12616943	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16866323	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2276619	0.83[EUR][1000 genomes]
rs2276620	0.83[EUR][1000 genomes]
rs3731756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3731758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3765020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3816073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4491754	0.83[EUR][1000 genomes]
rs55714261	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55821514	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56065555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56165369	1.00[AMR][1000 genomes]
rs56233214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56357262	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56367852	0.83[AMR][1000 genomes]
rs6734446	0.83[EUR][1000 genomes]
rs6736173	0.83[EUR][1000 genomes]
rs6736304	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73034346	0.83[EUR][1000 genomes]
rs73034359	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73034362	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73034364	0.83[EUR][1000 genomes]
rs73034377	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7584420	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179316800-179329000	Weak transcription	Liver	Liver
2	chr2:179316800-179329400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:179316800-179329800	Weak transcription	Ovary	ovary
4	chr2:179316800-179338200	Weak transcription	Fetal Stomach	stomach
5	chr2:179316800-179338800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:179316800-179341800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:179316800-179342400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr2:179316800-179342600	Weak transcription	Aorta	Aorta
9	chr2:179316800-179342800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:179317000-179329000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:179317000-179342000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:179317200-179328800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:179317200-179329200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:179317200-179329200	Weak transcription	Dnd41	blood
15	chr2:179317200-179342800	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:179317400-179341200	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:179317400-179341600	Weak transcription	GM12878-XiMat	blood
18	chr2:179317800-179329200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:179317800-179329200	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:179317800-179338200	Weak transcription	Osteobl	bone
21	chr2:179318000-179329200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:179318000-179332400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:179318000-179334200	Weak transcription	Fetal Kidney	kidney
24	chr2:179318000-179342800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:179320200-179329200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:179320800-179329400	Weak transcription	NH-A	brain
27	chr2:179321000-179329000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:179321200-179329400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:179321200-179342400	Weak transcription	HSMM	muscle
30	chr2:179321200-179342400	Weak transcription	HSMMtube	muscle
31	chr2:179322400-179329200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:179322800-179339000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:179323000-179328800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:179323600-179328400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:179323600-179329400	Weak transcription	Fetal Lung	lung
36	chr2:179324400-179329400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:179324600-179338200	Weak transcription	Fetal Brain Male	brain
38	chr2:179324800-179329000	Weak transcription	Primary B cells from cord blood	blood
39	chr2:179325000-179338800	Weak transcription	Left Ventricle	heart
40	chr2:179325200-179332200	Weak transcription	Fetal Intestine Large	intestine
41	chr2:179325600-179329200	Weak transcription	Fetal Brain Female	brain
42	chr2:179325600-179342000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:179325800-179338800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr2:179326200-179342000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:179326200-179342400	Weak transcription	Adipose Nuclei	Adipose
46	chr2:179326200-179342600	Weak transcription	Primary T cells from cord blood	blood
47	chr2:179327000-179342400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:179327200-179329200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:179327200-179341800	Weak transcription	NHLF	lung
50	chr2:179327200-179342400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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