Variant report

Variant	rs6494138
Chromosome Location	chr15:59983699-59983700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:78)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:78 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:59983506-59983866	HCT-116	colon:	n/a	n/a
2	RAD21	chr15:59983324-59983861	HCT-116	colon:	n/a	n/a
3	RAD21	chr15:59983347-59983738	MCF-7	breast:	n/a	n/a
4	CTCF	chr15:59983393-59983783	MCF-7	breast:	n/a	n/a
5	CTCF	chr15:59983492-59983737	A549	lung:	n/a	n/a
6	CTCF	chr15:59983560-59983710	GM12867	blood:	n/a	n/a
7	CTCF	chr15:59983560-59983710	AG04450	lung:	n/a	n/a
8	CTCF	chr15:59983466-59983727	Medullo	brain:	n/a	n/a
9	CTCF	chr15:59980032-59984022	A549	lung:	n/a	n/a
10	RAD21	chr15:59983345-59983861	HCT-116	colon:	n/a	n/a
11	RAD21	chr15:59983438-59983780	HepG2	liver:	n/a	n/a
12	CTCF	chr15:59983431-59983766	A549	lung:	n/a	n/a
13	RAD21	chr15:59983439-59983751	K562	blood:	n/a	n/a
14	CTCF	chr15:59983472-59983733	Lung_OC	lung:	n/a	n/a
15	RAD21	chr15:59983410-59983799	SK-N-SH_RA	brain:	n/a	n/a
16	RAD21	chr15:59983434-59983814	H1-hESC	embryonic stem cell:	n/a	n/a
17	IRF3	chr15:59983576-59983706	GM12878	blood:	n/a	chr15:59983671-59983680
18	RAD21	chr15:59983448-59983788	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr15:59983243-59983840	SK-N-SH	brain:	n/a	n/a
20	ZNF384	chr15:59983354-59983829	GM12878	blood:	n/a	n/a
21	CTCF	chr15:59983477-59983749	Spleen_OC	spleen:	n/a	n/a
22	CTCF	chr15:59983560-59983710	AG10803	skin:	n/a	n/a
23	CTCF	chr15:59983580-59983730	BJ	skin:	n/a	n/a
24	RAD21	chr15:59983473-59983706	GM12878	blood:	n/a	n/a
25	CTCF	chr15:59983431-59983780	K562	blood:	n/a	n/a
26	CTCF	chr15:59983486-59983719	K562	blood:	n/a	n/a
27	CTCF	chr15:59983499-59983702	GM10248	blood:	n/a	n/a
28	CTCF	chr15:59983500-59983790	MCF-7	breast:	n/a	n/a
29	CTCF	chr15:59983488-59983726	GM12878	blood:	n/a	n/a
30	CTCF	chr15:59983560-59983710	HBMEC	blood vessel:	n/a	n/a
31	CTCF	chr15:59983560-59983710	WI-38	lung:	n/a	n/a
32	CTCF	chr15:59983452-59983749	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr15:59983340-59983804	MCF10A-Er-Src	breast:	n/a	n/a
34	CTCF	chr15:59983580-59983730	HAc	cerebellar:	n/a	n/a
35	RAD21	chr15:59983393-59983746	ECC-1	luminal epithelium:	n/a	n/a
36	CTCF	chr15:59983560-59983710	NHEK	skin:	n/a	n/a
37	CTCF	chr15:59983497-59983707	LNCaP	prostate:	n/a	n/a
38	CTCF	chr15:59983560-59983710	GM12875	blood:	n/a	n/a
39	CTCF	chr15:59983499-59983701	Hela-S3	cervix:	n/a	n/a
40	RAD21	chr15:59983402-59983721	H1-hESC	embryonic stem cell:	n/a	n/a
41	RAD21	chr15:59983386-59983806	IMR90	lung:	n/a	n/a
42	RAD21	chr15:59983348-59983840	MCF-7	breast:	n/a	n/a
43	CTCF	chr15:59983497-59983734	SK-N-SH_RA	brain:	n/a	n/a
44	ZNF143	chr15:59983451-59983770	GM12878	blood:	n/a	n/a
45	RFX5	chr15:59983430-59983775	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr15:59983600-59983750	SAEC	small airway:	n/a	n/a
47	RAD21	chr15:59983353-59983839	ECC-1	luminal epithelium:	n/a	n/a
48	CTCF	chr15:59983580-59983730	Hela-S3	cervix:	n/a	n/a
49	RAD21	chr15:59983397-59983817	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr15:59983560-59983710	AG09319	gingival:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:59979548..59984505-chr15:60688391..60691990,7	K562	blood:
2	chr15:59946363..59951356-chr15:59979923..59984049,7	K562	blood:
3	chr15:59982442..59985079-chr15:60617660..60619822,3	K562	blood:
4	chr15:59983231..59984005-chr15:60618723..60619489,3	K562	blood:
5	chr15:59945879..59953077-chr15:59978622..59984049,13	K562	blood:
6	chr15:59982661..59985453-chr15:60307670..60309447,2	K562	blood:
7	chr15:59981413..59984505-chr15:60688549..60691597,3	K562	blood:

No data

Variant related genes	Relation type
BNIP2	TF binding region
ENSG00000140307	Chromatin interaction
ENSG00000182718	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1002181	0.83[ASN][1000 genomes]
rs10152431	0.81[AFR][1000 genomes]
rs10152791	0.82[AFR][1000 genomes]
rs10162629	0.83[ASN][1000 genomes]
rs1046053	0.82[ASN][1000 genomes]
rs11071468	0.83[ASN][1000 genomes]
rs11071469	0.83[ASN][1000 genomes]
rs11071471	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11629681	0.80[EUR][1000 genomes]
rs11634157	0.82[EUR][1000 genomes]
rs12438078	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12439645	0.81[EUR][1000 genomes]
rs12439658	0.80[EUR][1000 genomes]
rs12439707	0.80[EUR][1000 genomes]
rs12440020	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442896	0.88[EUR][1000 genomes]
rs12443242	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443297	0.89[EUR][1000 genomes]
rs12593480	0.83[ASN][1000 genomes]
rs12903647	0.82[ASN][1000 genomes]
rs12904505	0.82[EUR][1000 genomes]
rs12907554	0.83[ASN][1000 genomes]
rs12910451	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379702	0.81[AFR][1000 genomes]
rs13380147	0.83[AFR][1000 genomes]
rs1552031	0.83[ASN][1000 genomes]
rs16941645	0.85[AFR][1000 genomes]
rs16941648	0.82[AFR][1000 genomes]
rs17191002	0.80[EUR][1000 genomes]
rs17236804	0.85[ASN][1000 genomes]
rs17236867	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1871504	0.90[EUR][1000 genomes]
rs2306357	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306358	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307272	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2307275	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3087328	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3843695	0.83[EUR][1000 genomes]
rs3848119	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3936513	0.84[EUR][1000 genomes]
rs4533213	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4775195	0.82[ASN][1000 genomes]
rs4775200	0.82[EUR][1000 genomes]
rs56141740	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151440	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151441	0.90[EUR][1000 genomes]
rs6151442	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151444	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151445	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151446	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151447	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151448	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151449	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151450	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151451	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6151458	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151459	0.81[ASN][1000 genomes]
rs6151460	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151461	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151462	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6151467	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151470	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151472	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6151474	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6151477	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6151486	0.85[ASN][1000 genomes]
rs6151491	0.85[ASN][1000 genomes]
rs6151494	0.85[ASN][1000 genomes]
rs6151496	0.85[ASN][1000 genomes]
rs6151501	0.84[ASN][1000 genomes]
rs6151503	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151504	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151506	0.84[ASN][1000 genomes]
rs6151514	0.83[ASN][1000 genomes]
rs6151528	0.81[ASN][1000 genomes]
rs6151529	0.83[ASN][1000 genomes]
rs6151532	0.83[ASN][1000 genomes]
rs6151533	0.83[ASN][1000 genomes]
rs6151535	0.83[ASN][1000 genomes]
rs6151536	0.83[ASN][1000 genomes]
rs6151542	0.83[ASN][1000 genomes]
rs6151545	0.83[ASN][1000 genomes]
rs6494133	0.82[ASN][1000 genomes]
rs6494139	0.89[EUR][1000 genomes]
rs6494140	0.82[EUR][1000 genomes]
rs67712565	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67820349	0.83[ASN][1000 genomes]
rs7162645	0.82[EUR][1000 genomes]
rs7173534	0.89[EUR][1000 genomes]
rs7173827	0.89[EUR][1000 genomes]
rs7178211	0.89[EUR][1000 genomes]
rs722163	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs722164	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72625734	0.82[AFR][1000 genomes]
rs728037	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs728038	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs754641	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs754642	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754643	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755605	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025415	0.82[AFR][1000 genomes]
rs8026680	0.82[AFR][1000 genomes]
rs8027353	0.80[AFR][1000 genomes]
rs8027389	0.80[AFR][1000 genomes]
rs8027415	0.80[AFR][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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1824522	chr15:59919844-59987181	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6494138	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL
rs6494138	GTF2A2	cis	Whole Blood	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59982200-59986600	Weak transcription	Stomach Mucosa	stomach
2	chr15:59982400-59984200	Enhancers	Primary B cells from peripheral blood	blood
3	chr15:59982600-59987200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:59982800-59983800	Enhancers	Primary B cells from cord blood	blood
5	chr15:59982800-59983800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:59982800-59984000	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr15:59982800-59984200	Enhancers	Liver	Liver
8	chr15:59982800-59986400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:59983200-59986800	Weak transcription	Fetal Intestine Large	intestine
10	chr15:59983400-59985000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr15:59983600-59985200	Weak transcription	Hela-S3	cervix
12	chr15:59983600-59986800	Weak transcription	A549	lung

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