Variant report

Variant	rs6151441
Chromosome Location	chr15:59980548-59980549
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:67)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:67 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:59980530-59981886	GM12878	blood:	n/a	n/a
2	TBP	chr15:59980282-59981042	Hela-S3	cervix:	n/a	n/a
3	ELK1	chr15:59980051-59980863	K562	blood:	n/a	chr15:59980291-59980300 chr15:59980291-59980300
4	POLR2A	chr15:59980050-59982314	NB4	blood:	n/a	n/a
5	BRCA1	chr15:59980439-59982136	Hela-S3	cervix:	n/a	n/a
6	MXI1	chr15:59980247-59981945	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr15:59980389-59982367	Hela-S3	cervix:	n/a	n/a
8	IRF1	chr15:59980085-59981955	K562	blood:	n/a	chr15:59981805-59981819 chr15:59981815-59981828
9	CTCF	chr15:59980032-59984022	A549	lung:	n/a	n/a
10	POLR2A	chr15:59980521-59981988	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr15:59979986-59982227	GM12878	blood:	n/a	n/a
12	GABPA	chr15:59979737-59981942	A549	lung:	n/a	n/a
13	GATA2	chr15:59980022-59980745	HUVEC	blood vessel:	n/a	n/a
14	ELK1	chr15:59980029-59981849	GM12878	blood:	n/a	chr15:59980291-59980300 chr15:59980291-59980300
15	POLR2A	chr15:59979315-59982513	MCF10A-Er-Src	breast:	n/a	n/a
16	PML	chr15:59980471-59982000	GM12878	blood:	n/a	n/a
17	MXI1	chr15:59979968-59982637	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr15:59979869-59982333	HUVEC	blood vessel:	n/a	n/a
19	REST	chr15:59980481-59982028	H1-neurons	neurons:	n/a	n/a
20	CEBPB	chr15:59980506-59981061	Hela-S3	cervix:	n/a	n/a
21	TCF12	chr15:59980542-59982638	A549	lung:	n/a	n/a
22	ELF1	chr15:59980516-59981325	A549	lung:	n/a	n/a
23	GABPA	chr15:59980451-59981910	A549	lung:	n/a	n/a
24	IRF1	chr15:59980498-59981189	K562	blood:	n/a	n/a
25	GABPA	chr15:59980053-59980568	MCF-7	breast:	n/a	n/a
26	POLR2A	chr15:59979865-59982169	GM12891	blood:	n/a	n/a
27	CHD1	chr15:59980233-59980938	GM12878	blood:	n/a	n/a
28	POLR2A	chr15:59979863-59982314	Hela-S3	cervix:	n/a	n/a
29	GATA1	chr15:59979887-59982469	PBDE	blood:	n/a	n/a
30	ELK1	chr15:59980145-59981896	Hela-S3	cervix:	n/a	chr15:59980291-59980300 chr15:59980291-59980300
31	POLR2A	chr15:59980531-59982116	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr15:59980495-59982332	HUVEC	blood vessel:	n/a	n/a
33	FOS	chr15:59980522-59980845	MCF10A-Er-Src	breast:	n/a	n/a
34	TBP	chr15:59980046-59981204	GM12878	blood:	n/a	n/a
35	HCFC1	chr15:59980047-59982663	Hela-S3	cervix:	n/a	n/a
36	TBL1XR1	chr15:59979883-59981049	K562	blood:	n/a	n/a
37	POLR2A	chr15:59980548-59981928	HUVEC	blood vessel:	n/a	n/a
38	JUN	chr15:59979681-59982479	K562	blood:	n/a	n/a
39	REST	chr15:59980439-59982160	HL-60	blood:	n/a	n/a
40	POLR2A	chr15:59980147-59982210	GM12892	blood:	n/a	n/a
41	POLR2A	chr15:59979847-59982081	K562	blood:	n/a	n/a
42	EP300	chr15:59980514-59981326	GM12878	blood:	n/a	n/a
43	POLR2A	chr15:59980546-59982326	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr15:59980038-59982315	HL-60	blood:	n/a	n/a
45	EP300	chr15:59980130-59982296	K562	blood:	n/a	chr15:59980292-59980299
46	MYC	chr15:59980029-59982309	NB4	blood:	n/a	n/a
47	ELF1	chr15:59980532-59981937	A549	lung:	n/a	n/a
48	HEY1	chr15:59980522-59982326	K562	blood:	n/a	n/a
49	GABPA	chr15:59980503-59981987	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr15:59980281-59982276	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:59979537..59981515-chr15:60770595..60772119,2	K562	blood:
2	chr15:59979548..59984505-chr15:60688391..60691990,7	K562	blood:
3	chr15:59946363..59951356-chr15:59979923..59984049,7	K562	blood:
4	chr15:59979537..59982042-chr15:60770595..60772312,3	K562	blood:
5	chr15:59947605..59950537-chr15:59979625..59981765,3	MCF-7	breast:
6	chr15:59970781..59973494-chr15:59980091..59981802,2	MCF-7	breast:
7	chr15:59945879..59953077-chr15:59978622..59984049,13	K562	blood:
8	chr15:59979503..59981285-chr3:183330477..183331977,2	K562	blood:
9	chr15:59980114..59982040-chr15:60675665..60677456,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000259238	TF binding region
ENSG00000243584	Chromatin interaction
ENSG00000140307	Chromatin interaction
ENSG00000182718	Chromatin interaction
ENSG00000140299	Chromatin interaction
ENSG00000128915	Chromatin interaction
ENSG00000245534	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11071471	0.83[EUR][1000 genomes]
rs11629681	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11634157	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11637359	0.80[CHB][hapmap]
rs12438078	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs12439645	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12439658	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12439707	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12440020	0.89[EUR][1000 genomes]
rs12442896	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12443242	0.89[EUR][1000 genomes]
rs12443297	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904505	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12910451	0.90[EUR][1000 genomes]
rs17191002	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1871499	0.81[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap]
rs1871503	0.82[AMR][1000 genomes]
rs1871504	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2101019	0.89[YRI][hapmap]
rs2306357	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2306358	0.90[EUR][1000 genomes]
rs2307273	0.90[JPT][hapmap]
rs2899649	0.89[JPT][hapmap];0.84[YRI][hapmap]
rs3087328	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs3825870	0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap]
rs3843695	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3912205	0.92[AMR][1000 genomes]
rs3912206	0.86[AMR][1000 genomes]
rs3936513	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4270113	0.90[JPT][hapmap];0.89[YRI][hapmap]
rs4775200	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56141740	0.89[EUR][1000 genomes]
rs6151440	0.90[EUR][1000 genomes]
rs6151442	0.90[EUR][1000 genomes]
rs6151444	0.90[EUR][1000 genomes]
rs6151445	0.90[EUR][1000 genomes]
rs6151446	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6151447	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs6151448	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6151449	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs6151450	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6151451	0.90[EUR][1000 genomes]
rs6151483	0.80[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs6151487	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6151510	0.81[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs6151525	0.90[JPT][hapmap]
rs6151551	0.90[JPT][hapmap]
rs6151553	0.86[JPT][hapmap];0.80[YRI][hapmap]
rs6151561	0.80[CHB][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap]
rs6494138	0.90[EUR][1000 genomes]
rs6494139	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6494140	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7162645	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7173534	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7173827	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7178211	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs728037	0.88[EUR][1000 genomes]
rs728038	0.88[EUR][1000 genomes]
rs754641	0.87[EUR][1000 genomes]
rs754642	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs754643	0.90[EUR][1000 genomes]
rs755605	0.90[EUR][1000 genomes]
rs7882	1.00[JPT][hapmap];0.85[YRI][hapmap]
rs8026404	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][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
rs6151441	GTF2A2	cis	Whole Blood	GTEx
rs6151441	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59977200-59981000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr15:59977800-59980600	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr15:59977800-59980800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:59977800-59981000	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr15:59978200-59981000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr15:59978400-59980600	Enhancers	Small Intestine	intestine
7	chr15:59979400-59980600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr15:59979400-59980600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr15:59979600-59980600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr15:59979600-59980600	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr15:59979600-59980600	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr15:59979600-59980600	Enhancers	Spleen	Spleen
13	chr15:59979600-59980600	Flanking Active TSS	Hela-S3	cervix
14	chr15:59979600-59980800	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr15:59979600-59981200	Active TSS	Right Atrium	heart
16	chr15:59979600-59982400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr15:59979600-59982400	Active TSS	GM12878-XiMat	blood
18	chr15:59979600-59982400	Active TSS	HSMMtube	muscle
19	chr15:59979800-59980600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr15:59979800-59980600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:59979800-59980600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:59979800-59980600	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr15:59979800-59980600	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr15:59979800-59980600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr15:59979800-59980600	Flanking Active TSS	Fetal Brain Male	brain
26	chr15:59979800-59980600	Flanking Active TSS	Fetal Lung	lung
27	chr15:59979800-59980600	Flanking Active TSS	Rectal Smooth Muscle	rectum
28	chr15:59979800-59980600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr15:59979800-59980600	Flanking Active TSS	NH-A	brain
30	chr15:59979800-59980800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr15:59979800-59982400	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr15:59979800-59982400	Active TSS	Left Ventricle	heart
33	chr15:59979800-59982600	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr15:59979800-59982600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:59980000-59980600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:59980000-59980600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr15:59980000-59980600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr15:59980000-59980600	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr15:59980000-59980600	Flanking Active TSS	Fetal Heart	heart
40	chr15:59980000-59980600	Flanking Active TSS	Fetal Kidney	kidney
41	chr15:59980000-59980600	Flanking Active TSS	Fetal Stomach	stomach
42	chr15:59980000-59980800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:59980000-59982200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr15:59980000-59982200	Active TSS	Colonic Mucosa	Colon
45	chr15:59980000-59982200	Active TSS	Lung	lung
46	chr15:59980000-59982400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:59980000-59982400	Active TSS	Fetal Muscle Trunk	muscle
48	chr15:59980000-59982600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:59980000-59982600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:59980000-59982600	Active TSS	Ovary	ovary

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