Variant report

Variant	rs12616200
Chromosome Location	chr2:128252778-128252779
allele	A/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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:128244656..128249813-chr2:128251598..128254709,4	K562	blood:
2	chr2:128246179..128248440-chr2:128251360..128253432,3	MCF-7	breast:
3	chr2:128234838..128237343-chr2:128250222..128254219,3	K562	blood:
4	chr2:128252742..128257786-chr2:128259885..128265839,7	K562	blood:
5	chr2:128252742..128255070-chr2:128263163..128265839,2	K562	blood:
6	chr2:128248313..128249963-chr2:128250526..128253309,2	K562	blood:
7	chr2:128234838..128236563-chr2:128251680..128254219,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163166	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10496663	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10928769	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11681225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11682864	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11685630	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11690086	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11892245	0.81[ASN][1000 genomes]
rs12053309	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12233101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12616100	0.82[ASN][1000 genomes]
rs12618494	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12619773	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12620037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015274	0.95[AFR][1000 genomes]
rs17015334	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015401	0.83[ASN][1000 genomes]
rs1864553	0.83[ASN][1000 genomes]
rs2082182	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2099209	0.82[ASN][1000 genomes]
rs2288655	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35208523	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3732205	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3889307	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55688542	0.81[EUR][1000 genomes]
rs56100618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56261855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56327685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62156572	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62156576	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62156599	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6758364	0.82[ASN][1000 genomes]
rs72843327	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7586672	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs777556	0.99[ASN][1000 genomes]
rs873099	0.82[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	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12616200	AC068282.3	cis	Thyroid	GTEx
rs12616200	AC068282.3	cis	Muscle Skeletal	GTEx
rs12616200	AC068282.3	cis	Esophagus Mucosa	GTEx
rs12616200	AC068282.3	cis	Esophagus Muscularis	GTEx
rs12616200	AC068282.3	cis	Nerve Tibial	GTEx
rs12616200	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs12616200	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12616200	AC068282.3	cis	Whole Blood	GTEx
rs12616200	AC068282.3	cis	Artery Tibial	GTEx
rs12616200	AC068282.3	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128223600-128268800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:128229000-128257000	Weak transcription	Stomach Mucosa	stomach
3	chr2:128235200-128270000	Strong transcription	Dnd41	blood
4	chr2:128237400-128262400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:128237600-128255000	Strong transcription	Fetal Muscle Leg	muscle
6	chr2:128237600-128255200	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr2:128237600-128255400	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:128237600-128256000	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:128237600-128256200	Strong transcription	HepG2	liver
10	chr2:128237600-128263200	Strong transcription	Adipose Nuclei	Adipose
11	chr2:128237600-128263200	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr2:128237600-128263400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:128237600-128263400	Strong transcription	Fetal Thymus	thymus
14	chr2:128237800-128254400	Strong transcription	Brain Substantia Nigra	brain
15	chr2:128237800-128254600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:128237800-128255800	Strong transcription	Stomach Smooth Muscle	stomach
17	chr2:128237800-128263200	Strong transcription	Liver	Liver
18	chr2:128237800-128263200	Strong transcription	HUVEC	blood vessel
19	chr2:128237800-128263400	Strong transcription	Placenta	Placenta
20	chr2:128238400-128255200	Strong transcription	K562	blood
21	chr2:128238400-128262400	Strong transcription	NH-A	brain
22	chr2:128238800-128260400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr2:128239200-128263400	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr2:128239200-128264800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:128239400-128255400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:128239400-128256200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:128239400-128264400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:128239400-128266200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:128239400-128266400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:128239800-128261800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:128240000-128263400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:128240200-128263600	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:128240400-128263800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:128240600-128265600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:128241000-128263200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:128241600-128253800	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:128241600-128254800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:128241800-128254600	Strong transcription	HSMMtube	muscle
39	chr2:128242000-128253800	Strong transcription	Fetal Lung	lung
40	chr2:128242000-128254200	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr2:128242000-128256600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:128242000-128262600	Strong transcription	Fetal Brain Female	brain
43	chr2:128242600-128255800	Strong transcription	NHDF-Ad	bronchial
44	chr2:128242600-128263200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:128242600-128263200	Strong transcription	HMEC	breast
46	chr2:128242800-128262200	Strong transcription	HSMM	muscle
47	chr2:128244000-128254800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:128244000-128263200	Strong transcription	Primary B cells from cord blood	blood
49	chr2:128244400-128255800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:128244600-128255600	Strong transcription	Primary neutrophils fromperipheralblood	blood

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