Variant report

Variant	rs1656895
Chromosome Location	chr15:40224107-40224108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr15:40223900-40224137	K562	blood:	n/a	n/a
2	CTCF	chr15:40224000-40224150	HVMF	connective:	n/a	n/a
3	CTCF	chr15:40223980-40224130	HCT-116	colon:	n/a	n/a
4	CTCF	chr15:40223960-40224110	AG10803	skin:	n/a	n/a
5	RAD21	chr15:40223825-40224220	A549	lung:	n/a	n/a
6	CTCF	chr15:40224000-40224150	BJ	skin:	n/a	n/a
7	RAD21	chr15:40223724-40224137	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr15:40223960-40224110	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr15:40223885-40224192	A549	lung:	n/a	n/a
10	CTCF	chr15:40223960-40224110	HUVEC	blood vessel:	n/a	n/a
11	CTCF	chr15:40223960-40224110	BJ	skin:	n/a	n/a
12	RAD21	chr15:40223864-40224135	A549	lung:	n/a	n/a
13	CTCF	chr15:40223960-40224110	HVMF	connective:	n/a	n/a
14	RAD21	chr15:40223828-40224195	A549	lung:	n/a	n/a
15	CTCF	chr15:40223825-40224180	IMR90	lung:	n/a	n/a
16	RAD21	chr15:40223860-40224172	IMR90	lung:	n/a	n/a
17	RAD21	chr15:40223834-40224177	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr15:40223960-40224110	HBMEC	blood vessel:	n/a	n/a
19	CTCF	chr15:40223960-40224110	AG09309	skin:	n/a	n/a
20	RAD21	chr15:40223705-40224131	MCF-7	breast:	n/a	n/a
21	RAD21	chr15:40223838-40224112	K562	blood:	n/a	n/a
22	CTCF	chr15:40223960-40224110	HPF	lung:	n/a	n/a
23	CTCF	chr15:40223960-40224110	HCM	heart:	n/a	n/a
24	RAD21	chr15:40223864-40224107	Hela-S3	cervix:	n/a	n/a
25	RAD21	chr15:40223853-40224152	H1-hESC	embryonic stem cell:	n/a	n/a
26	RAD21	chr15:40223768-40224257	HCT-116	colon:	n/a	n/a
27	CTCF	chr15:40223960-40224110	HCPEpiC	choroid plexus:	n/a	n/a
28	CTCF	chr15:40223980-40224130	GM12874	blood:	n/a	n/a
29	CTCF	chr15:40223824-40224108	A549	lung:	n/a	n/a
30	CTCF	chr15:40223846-40224175	K562	blood:	n/a	n/a
31	CTCF	chr15:40224020-40224170	Caco-2	colon:	n/a	n/a
32	CTCF	chr15:40224020-40224170	HFF-Myc	foreskin:	n/a	n/a
33	RAD21	chr15:40223590-40224236	SK-N-SH	brain:	n/a	n/a
34	CTCF	chr15:40223960-40224110	AG09319	gingival:	n/a	n/a
35	CTCF	chr15:40224000-40224150	HMEC	breast:	n/a	n/a
36	RAD21	chr15:40223806-40224167	HepG2	liver:	n/a	n/a
37	CTCF	chr15:40223627-40224334	A549	lung:	n/a	n/a
38	CTCF	chr15:40223896-40224107	A549	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40222962..40225062-chr15:40343455..40345112,2	K562	blood:
2	chr15:40214834..40219458-chr15:40222098..40228403,10	K562	blood:
3	chr15:40209081..40211622-chr15:40223398..40225588,2	K562	blood:
4	chr15:40214696..40216721-chr15:40223722..40226672,2	MCF-7	breast:
5	chr15:40211366..40214080-chr15:40223428..40228644,6	MCF-7	breast:

No data

Variant related genes	Relation type
EIF2AK4	TF binding region
ENSG00000166073	Chromatin interaction
ENSG00000200305	Chromatin interaction
ENSG00000246863	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12439335	0.87[ASN][1000 genomes]
rs1656894	0.87[ASN][1000 genomes]
rs1656896	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2247984	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412451	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2917497	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2934194	0.89[ASN][1000 genomes]
rs480095	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489424	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494614	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494690	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500200	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs508281	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs518770	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524240	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs525910	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs527610	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs534757	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535407	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs552251	0.89[ASN][1000 genomes]
rs562159	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577289	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs580836	0.82[ASN][1000 genomes]
rs581233	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv832983	chr15:40098766-40248839	Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1656895	EIF2AK4	cis	Artery Tibial	GTEx
rs1656895	EIF2AK4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40213600-40225000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:40213600-40225400	Weak transcription	Pancreas	Pancrea
3	chr15:40213800-40225800	Weak transcription	Right Atrium	heart
4	chr15:40215200-40226000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:40215600-40225800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:40218200-40224800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:40218200-40225000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr15:40218400-40224200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:40218400-40224800	Weak transcription	Hela-S3	cervix
10	chr15:40219000-40224800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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