Variant report

Variant	rs17137491
Chromosome Location	chr6:4018568-4018569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr6:4018423-4019238	MCF-7	breast:	n/a	n/a
2	POLR2A	chr6:4018361-4019186	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF1	chr6:4018274-4019292	H1-neurons	neurons:	n/a	n/a
4	CHD2	chr6:4018535-4019209	GM12878	blood:	n/a	chr6:4018870-4018880
5	ETS1	chr6:4018383-4019213	K562	blood:	n/a	chr6:4019003-4019014 chr6:4018735-4018746
6	CEBPB	chr6:4018157-4019435	Hela-S3	cervix:	n/a	n/a
7	IRF1	chr6:4017696-4020054	K562	blood:	n/a	chr6:4019378-4019385 chr6:4018999-4019013
8	TAF1	chr6:4018323-4019382	K562	blood:	n/a	n/a
9	SIN3AK20	chr6:4017963-4019674	MCF-7	breast:	n/a	n/a
10	POLR2A	chr6:4018499-4019263	Gliobla	brain:	n/a	n/a
11	POLR2A	chr6:4018351-4019343	HCT-116	colon:	n/a	n/a
12	TAF1	chr6:4018164-4019242	Hela-S3	cervix:	n/a	n/a
13	E2F6	chr6:4018411-4018719	K562	blood:	n/a	chr6:4018524-4018534
14	MYC	chr6:4018501-4018572	MCF-7	breast:	n/a	n/a
15	ELK1	chr6:4018261-4019138	K562	blood:	n/a	n/a
16	POLR2A	chr6:4018068-4019636	K562	blood:	n/a	n/a
17	YY1	chr6:4018409-4019179	H1-hESC	embryonic stem cell:	n/a	chr6:4019003-4019012 chr6:4018685-4018699 chr6:4018621-4018630 chr6:4018735-4018744 chr6:4019001-4019015 chr6:4018736-4018750 chr6:4018615-4018629
18	POLR2A	chr6:4017992-4019741	K562	blood:	n/a	n/a
19	YY1	chr6:4018365-4019194	K562	blood:	n/a	chr6:4019003-4019012 chr6:4018685-4018699 chr6:4018621-4018630 chr6:4018735-4018744 chr6:4019001-4019015 chr6:4018736-4018750 chr6:4018615-4018629
20	SMARCB1	chr6:4018249-4019251	Hela-S3	cervix:	n/a	n/a
21	RELA	chr6:4018064-4019251	GM15510	blood:	n/a	n/a
22	CEBPB	chr6:4018545-4019354	HepG2	liver:	n/a	n/a
23	POLR2A	chr6:4017981-4019968	K562	blood:	n/a	n/a
24	PBX3	chr6:4017979-4019152	SK-N-SH	brain:	n/a	chr6:4018309-4018320
25	POLR2A	chr6:4018374-4019306	H1-neurons	neurons:	n/a	n/a
26	NFIC	chr6:4018363-4019230	ECC-1	luminal epithelium:	n/a	n/a
27	SIN3AK20	chr6:4018475-4019266	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr6:4017591-4019463	HepG2	liver:	n/a	n/a
29	POLR2A	chr6:4018563-4019258	GM10847	blood:	n/a	n/a
30	BCLAF1	chr6:4018262-4019291	GM12878	blood:	n/a	chr6:4018617-4018630 chr6:4018970-4018983 chr6:4018734-4018743 chr6:4018619-4018628 chr6:4018926-4018939
31	POU2F2	chr6:4018558-4019143	GM12878	blood:	n/a	chr6:4019003-4019015
32	YY1	chr6:4018428-4019118	ECC-1	luminal epithelium:	n/a	chr6:4019003-4019012 chr6:4018685-4018699 chr6:4018621-4018630 chr6:4018735-4018744 chr6:4019001-4019015 chr6:4018736-4018750 chr6:4018615-4018629
33	POLR2A	chr6:4017464-4019357	MCF10A-Er-Src	breast:	n/a	n/a
34	TBL1XR1	chr6:4018477-4019617	K562	blood:	n/a	n/a
35	CREB1	chr6:4018481-4019169	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr6:4018415-4019248	MCF-7	breast:	n/a	n/a
37	ZNF263	chr6:4018077-4019319	HEK293-T-REx	kidney:	n/a	chr6:4019122-4019131
38	POLR2A	chr6:4018352-4019323	K562	blood:	n/a	n/a
39	BRCA1	chr6:4018118-4019423	Hela-S3	cervix:	n/a	n/a
40	BHLHE40	chr6:4017344-4019273	GM12878	blood:	n/a	chr6:4018967-4018983 chr6:4018739-4018755 chr6:4018736-4018752 chr6:4018685-4018701 chr6:4018737-4018753
41	BCLAF1	chr6:4018418-4019270	GM12878	blood:	n/a	chr6:4018617-4018630 chr6:4018970-4018983 chr6:4018734-4018743 chr6:4018619-4018628 chr6:4018926-4018939
42	NFATC1	chr6:4018423-4019172	GM12878	blood:	n/a	n/a
43	RCOR1	chr6:4018342-4019519	Hela-S3	cervix:	n/a	n/a
44	TAF1	chr6:4018406-4019194	HepG2	liver:	n/a	n/a
45	YY1	chr6:4018383-4019193	K562	blood:	n/a	chr6:4019003-4019012 chr6:4018685-4018699 chr6:4018621-4018630 chr6:4018735-4018744 chr6:4019001-4019015 chr6:4018736-4018750 chr6:4018615-4018629
46	POLR2A	chr6:4018524-4019350	GM12892	blood:	n/a	n/a
47	CREB1	chr6:4018453-4019208	GM12878	blood:	n/a	n/a
48	ZNF143	chr6:4018242-4019460	K562	blood:	n/a	chr6:4018737-4018747
49	CHD1	chr6:4018036-4019260	GM12878	blood:	n/a	chr6:4018870-4018880
50	MAX	chr6:4018222-4019512	HCT-116	colon:	n/a	chr6:4019004-4019014 chr6:4019228-4019238

No.	Distal block	Cell Line	Cell type
1	chr6:3156268..3158209-chr6:4016480..4019162,2	K562	blood:
2	chr3:160282902..160283821-chr6:4018096..4018693,2	Hela-S3	cervix:
3	chr6:4016030..4019961-chr6:4020836..4023596,5	MCF-7	breast:
4	chr2:122406707..122407503-chr6:4018436..4018946,2	NB4	blood:
5	chr6:4016355..4024618-chr6:4131840..4138381,21	K562	blood:
6	chr1:11969213..11970271-chr6:4018298..4019376,3	Hela-S3	cervix:
7	chr6:4017302..4025509-chr6:4131840..4138381,19	K562	blood:
8	chr6:4016440..4019187-chr6:4054276..4058013,4	K562	blood:
9	chr1:211555727..211556435-chr6:4018361..4019306,2	Hela-S3	cervix:
10	chr6:3750661..3753306-chr6:4017495..4019534,2	MCF-7	breast:
11	chr1:36689783..36690762-chr6:4018381..4019093,2	Hela-S3	cervix:
12	chr6:2988870..2991161-chr6:4018285..4020823,2	K562	blood:
13	chr6:3117348..3119733-chr6:4017604..4019806,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf146-1	chr6:4016675-4018801	XLOC_005587
2	lnc-C6orf146-1	chr6:4006806-4020323	NONHSAT107264

Variant related genes	Relation type
ENSG00000272248	TF binding region
PRPF4B	TF binding region
ENSG00000236859	Chromatin interaction
ENSG00000201801	Chromatin interaction
ENSG00000137267	Chromatin interaction
ENSG00000112739	Chromatin interaction
ENSG00000244041	Chromatin interaction
ENSG00000198721	Chromatin interaction
ENSG00000270504	Chromatin interaction
ENSG00000254821	Chromatin interaction
ENSG00000186432	Chromatin interaction
ENSG00000229320	Chromatin interaction
ENSG00000137274	Chromatin interaction
ENSG00000124588	Chromatin interaction
ENSG00000054118	Chromatin interaction
ENSG00000234817	Chromatin interaction
ENSG00000168994	Chromatin interaction
ENSG00000153363	Chromatin interaction
ENSG00000074054	Chromatin interaction
ENSG00000230648	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12110567	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17137450	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67642293	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72841266	0.87[EUR][1000 genomes]
rs72841268	0.87[EUR][1000 genomes]
rs72841271	0.87[EUR][1000 genomes]
rs72841275	0.86[EUR][1000 genomes]
rs72841286	0.87[EUR][1000 genomes]
rs72841295	0.84[EUR][1000 genomes]
rs72845852	0.81[EUR][1000 genomes]
rs736859	0.89[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7755418	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9502110	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9503890	1.00[YRI][hapmap];0.91[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	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4017200-4019200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:4017400-4018600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:4017400-4018800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:4017400-4019000	Active TSS	Stomach Smooth Muscle	stomach
5	chr6:4017400-4019200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:4017400-4019200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:4017400-4019200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:4017400-4019200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:4017400-4019400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:4017400-4019400	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr6:4017400-4019400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:4017400-4019400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:4017400-4019400	Active TSS	Aorta	Aorta
14	chr6:4017400-4019400	Active TSS	A549	lung
15	chr6:4017400-4019400	Active TSS	NHLF	lung
16	chr6:4017400-4019800	Active TSS	H1 Cell Line	embryonic stem cell
17	chr6:4017400-4019800	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr6:4017400-4020000	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr6:4017400-4023000	Active TSS	K562	blood
20	chr6:4017600-4018600	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr6:4017600-4019200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:4017600-4019200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:4017600-4019200	Active TSS	Fetal Kidney	kidney
24	chr6:4017600-4019200	Active TSS	HSMMtube	muscle
25	chr6:4017600-4019400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr6:4017600-4019400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:4017600-4019400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:4017600-4019400	Active TSS	Psoas Muscle	Psoas
29	chr6:4017600-4019600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:4017600-4019800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:4017800-4018600	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr6:4017800-4018600	Active TSS	Right Atrium	heart
33	chr6:4017800-4019000	Active TSS	Primary T cells fromperipheralblood	blood
34	chr6:4017800-4019000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:4017800-4019000	Active TSS	HMEC	breast
36	chr6:4017800-4019200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:4017800-4019200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr6:4017800-4019200	Active TSS	Muscle Satellite Cultured Cells	--
39	chr6:4017800-4019200	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr6:4017800-4019200	Active TSS	Fetal Muscle Leg	muscle
41	chr6:4017800-4019200	Active TSS	Fetal Thymus	thymus
42	chr6:4017800-4019200	Active TSS	Thymus	Thymus
43	chr6:4017800-4019200	Active TSS	GM12878-XiMat	blood
44	chr6:4017800-4019200	Active TSS	Hela-S3	cervix
45	chr6:4017800-4019200	Bivalent/Poised TSS	HepG2	liver
46	chr6:4017800-4019200	Active TSS	HSMM	muscle
47	chr6:4017800-4019400	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr6:4017800-4019400	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr6:4017800-4019400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:4017800-4019400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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