Variant report

Variant	rs62183801
Chromosome Location	chr2:172867475-172867476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr2:172867330-172867617	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:172836942..172840182-chr2:172865086..172867545,3	K562	blood:
2	chr2:172866012..172868252-chr2:172888365..172889925,2	K562	blood:
3	chr2:172867339..172869674-chr2:172948065..172950386,2	K562	blood:
4	chr2:172859788..172868192-chr2:172944876..172951443,18	MCF-7	breast:
5	chr2:172866585..172869561-chr2:172917120..172919427,2	K562	blood:
6	chr2:172863189..172870519-chr2:172946500..172952655,22	K562	blood:
7	chr2:172747937..172750894-chr2:172866713..172868813,2	K562	blood:
8	chr2:172867067..172870652-chr2:172884225..172887785,3	K562	blood:
9	chr2:172866585..172869561-chr2:172915980..172919427,3	K562	blood:
10	chr2:172862808..172868920-chr2:172961807..172971063,13	K562	blood:

No data

Variant related genes	Relation type
SLC25A12	TF binding region
ENSG00000115844	Chromatin interaction
ENSG00000115840	Chromatin interaction
ENSG00000172878	Chromatin interaction
ENSG00000144355	Chromatin interaction
ENSG00000236651	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11676438	0.84[AMR][1000 genomes]
rs55653103	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62182436	0.85[AMR][1000 genomes]
rs62183769	0.87[AMR][1000 genomes]
rs62183770	0.87[AMR][1000 genomes]
rs62183782	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62183783	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62183784	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62183785	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62183800	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6718013	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6729945	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6730085	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6733794	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6737308	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6746701	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7557612	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7584187	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7598246	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[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	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv3031	chr2:172867462-172884232	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62183801	AC068039.4	cis	Muscle Skeletal	GTEx
rs62183801	AC068039.4	cis	Thyroid	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172865200-172886600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:172865400-172877200	Weak transcription	Pancreas	Pancrea
3	chr2:172865400-172878000	Weak transcription	Gastric	stomach
4	chr2:172865600-172869600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr2:172865600-172870400	Weak transcription	Right Ventricle	heart
6	chr2:172865600-172875200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr2:172865600-172876600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:172865600-172877200	Weak transcription	Psoas Muscle	Psoas
9	chr2:172865600-172878000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:172865600-172897400	Weak transcription	Primary T cells from cord blood	blood
11	chr2:172865800-172869000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:172865800-172869800	Weak transcription	Brain Anterior Caudate	brain
13	chr2:172865800-172876600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:172865800-172877200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:172865800-172877600	Weak transcription	Fetal Kidney	kidney
16	chr2:172865800-172878000	Weak transcription	Primary B cells from cord blood	blood
17	chr2:172865800-172886400	Weak transcription	Fetal Intestine Small	intestine
18	chr2:172865800-172886600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:172866000-172868800	Weak transcription	Stomach Mucosa	stomach
20	chr2:172866000-172872600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:172866000-172873600	Weak transcription	Fetal Lung	lung
22	chr2:172866000-172876400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:172866000-172877200	Weak transcription	Ovary	ovary
24	chr2:172866000-172877600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:172866000-172877800	Weak transcription	HSMM	muscle
26	chr2:172866000-172878000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr2:172866000-172886800	Weak transcription	HSMMtube	muscle
28	chr2:172866200-172876400	Weak transcription	Dnd41	blood
29	chr2:172866200-172877000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:172866400-172875800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:172866800-172882600	Weak transcription	K562	blood
32	chr2:172867400-172867600	Enhancers	Brain Germinal Matrix	brain

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