Variant report

Variant	rs17137488
Chromosome Location	chr6:4018332-4018333
allele	C/T
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	chr6:4018274-4019292	H1-neurons	neurons:	n/a	n/a
2	CEBPB	chr6:4018157-4019435	Hela-S3	cervix:	n/a	n/a
3	IRF1	chr6:4017696-4020054	K562	blood:	n/a	chr6:4019378-4019385 chr6:4018999-4019013
4	TAF1	chr6:4018323-4019382	K562	blood:	n/a	n/a
5	SIN3AK20	chr6:4017963-4019674	MCF-7	breast:	n/a	n/a
6	TAF1	chr6:4018164-4019242	Hela-S3	cervix:	n/a	n/a
7	ELK1	chr6:4018261-4019138	K562	blood:	n/a	n/a
8	POLR2A	chr6:4018068-4019636	K562	blood:	n/a	n/a
9	POLR2A	chr6:4017992-4019741	K562	blood:	n/a	n/a
10	SMARCB1	chr6:4018249-4019251	Hela-S3	cervix:	n/a	n/a
11	RELA	chr6:4018064-4019251	GM15510	blood:	n/a	n/a
12	POLR2A	chr6:4017981-4019968	K562	blood:	n/a	n/a
13	PBX3	chr6:4017979-4019152	SK-N-SH	brain:	n/a	chr6:4018309-4018320
14	YY1	chr6:4018053-4018423	SK-N-SH_RA	brain:	n/a	n/a
15	POLR2A	chr6:4017591-4019463	HepG2	liver:	n/a	n/a
16	BCLAF1	chr6:4018262-4019291	GM12878	blood:	n/a	chr6:4018617-4018630 chr6:4018970-4018983 chr6:4018734-4018743 chr6:4018619-4018628 chr6:4018926-4018939
17	POLR2A	chr6:4017464-4019357	MCF10A-Er-Src	breast:	n/a	n/a
18	ZNF263	chr6:4018077-4019319	HEK293-T-REx	kidney:	n/a	chr6:4019122-4019131
19	BRCA1	chr6:4018118-4019423	Hela-S3	cervix:	n/a	n/a
20	BHLHE40	chr6:4017344-4019273	GM12878	blood:	n/a	chr6:4018967-4018983 chr6:4018739-4018755 chr6:4018736-4018752 chr6:4018685-4018701 chr6:4018737-4018753
21	ZNF143	chr6:4018242-4019460	K562	blood:	n/a	chr6:4018737-4018747
22	CHD1	chr6:4018036-4019260	GM12878	blood:	n/a	chr6:4018870-4018880
23	MAX	chr6:4018222-4019512	HCT-116	colon:	n/a	chr6:4019004-4019014 chr6:4019228-4019238
24	CHD1	chr6:4018062-4019313	H1-hESC	embryonic stem cell:	n/a	chr6:4018870-4018880
25	EP300	chr6:4017373-4019459	GM12878	blood:	n/a	chr6:4019208-4019218 chr6:4018862-4018878 chr6:4019257-4019265 chr6:4019407-4019417 chr6:4018738-4018747 chr6:4018736-4018752 chr6:4018736-4018745
26	POLR2A	chr6:4017915-4019443	H1-hESC	embryonic stem cell:	n/a	n/a
27	PML	chr6:4018053-4019493	K562	blood:	n/a	n/a
28	TAF1	chr6:4018269-4019123	H1-neurons	neurons:	n/a	n/a
29	MYBL2	chr6:4018171-4019519	HepG2	liver:	n/a	n/a
30	POLR2A	chr6:4018103-4019296	H1-neurons	neurons:	n/a	n/a
31	POLR2A	chr6:4018220-4019333	GM12878	blood:	n/a	n/a
32	JUND	chr6:4018313-4019536	K562	blood:	n/a	chr6:4019027-4019036
33	SIN3A	chr6:4018099-4019480	H1-hESC	embryonic stem cell:	n/a	chr6:4018527-4018538
34	CCNT2	chr6:4018112-4019456	K562	blood:	n/a	chr6:4019003-4019012
35	POLR2A	chr6:4018052-4019338	GM18505	blood:	n/a	n/a
36	ARID3A	chr6:4017850-4019471	HepG2	liver:	n/a	n/a
37	HMGN3	chr6:4018112-4019394	K562	blood:	n/a	chr6:4018412-4018419
38	POLR2A	chr6:4018092-4019247	H1-hESC	embryonic stem cell:	n/a	n/a
39	USF2	chr6:4018325-4018983	H1-hESC	embryonic stem cell:	n/a	chr6:4018967-4018983 chr6:4018739-4018755 chr6:4018736-4018752 chr6:4018685-4018701 chr6:4018737-4018753
40	TAF1	chr6:4018165-4019368	PFSK-1	brain:	n/a	n/a
41	POLR2A	chr6:4018219-4019384	GM12892	blood:	n/a	n/a
42	TCF12	chr6:4018068-4019298	A549	lung:	n/a	n/a
43	RCOR1	chr6:4018201-4019635	K562	blood:	n/a	n/a
44	POLR2A	chr6:4017797-4019957	K562	blood:	n/a	n/a
45	CTCF	chr6:4018220-4018370	HMEC	breast:	n/a	n/a
46	POLR2A	chr6:4017736-4019403	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr6:4018273-4019272	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr6:4018055-4019365	HUVEC	blood vessel:	n/a	n/a
49	TBP	chr6:4018130-4019846	K562	blood:	n/a	n/a
50	BCLAF1	chr6:4018298-4020035	K562	blood:	n/a	chr6:4018617-4018630 chr6:4018970-4018983 chr6:4018734-4018743 chr6:4018619-4018628 chr6:4018926-4018939

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	chr6:4016355..4024618-chr6:4131840..4138381,21	K562	blood:
5	chr1:11969213..11970271-chr6:4018298..4019376,3	Hela-S3	cervix:
6	chr6:4017302..4025509-chr6:4131840..4138381,19	K562	blood:
7	chr6:4016440..4019187-chr6:4054276..4058013,4	K562	blood:
8	chr6:3750661..3753306-chr6:4017495..4019534,2	MCF-7	breast:
9	chr6:2988870..2991161-chr6:4018285..4020823,2	K562	blood:
10	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
ENSG00000201801	Chromatin interaction
ENSG00000112739	Chromatin interaction
ENSG00000230648	Chromatin interaction
ENSG00000270504	Chromatin interaction
ENSG00000124588	Chromatin interaction
ENSG00000186432	Chromatin interaction
ENSG00000137267	Chromatin interaction
ENSG00000198721	Chromatin interaction
ENSG00000254821	Chromatin interaction
ENSG00000234817	Chromatin interaction
ENSG00000137274	Chromatin interaction
ENSG00000168994	Chromatin interaction
ENSG00000229320	Chromatin interaction
ENSG00000244041	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10485175	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17733807	1.00[CEU][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.89[EUR][1000 genomes]
rs2147376	0.84[EUR][1000 genomes]
rs2181893	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35085092	0.91[EUR][1000 genomes]
rs41301865	0.86[EUR][1000 genomes]
rs6924737	0.85[CEU][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7767348	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[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	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	chr6:4011400-4018400	Weak transcription	Spleen	Spleen
2	chr6:4017200-4019200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:4017400-4018400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:4017400-4018400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr6:4017400-4018600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:4017400-4018800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:4017400-4019000	Active TSS	Stomach Smooth Muscle	stomach
8	chr6:4017400-4019200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:4017400-4019200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:4017400-4019200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:4017400-4019200	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr6:4017400-4019400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:4017400-4019400	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr6:4017400-4019400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:4017400-4019400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:4017400-4019400	Active TSS	Aorta	Aorta
17	chr6:4017400-4019400	Active TSS	A549	lung
18	chr6:4017400-4019400	Active TSS	NHLF	lung
19	chr6:4017400-4019800	Active TSS	H1 Cell Line	embryonic stem cell
20	chr6:4017400-4019800	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr6:4017400-4020000	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr6:4017400-4023000	Active TSS	K562	blood
23	chr6:4017600-4018600	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr6:4017600-4019200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:4017600-4019200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:4017600-4019200	Active TSS	Fetal Kidney	kidney
27	chr6:4017600-4019200	Active TSS	HSMMtube	muscle
28	chr6:4017600-4019400	Active TSS	H9 Cell Line	embryonic stem cell
29	chr6:4017600-4019400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:4017600-4019400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:4017600-4019400	Active TSS	Psoas Muscle	Psoas
32	chr6:4017600-4019600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr6:4017600-4019800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:4017800-4018400	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr6:4017800-4018400	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr6:4017800-4018400	Weak transcription	Gastric	stomach
37	chr6:4017800-4018400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr6:4017800-4018400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr6:4017800-4018600	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr6:4017800-4018600	Active TSS	Right Atrium	heart
41	chr6:4017800-4019000	Active TSS	Primary T cells fromperipheralblood	blood
42	chr6:4017800-4019000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:4017800-4019000	Active TSS	HMEC	breast
44	chr6:4017800-4019200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:4017800-4019200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr6:4017800-4019200	Active TSS	Muscle Satellite Cultured Cells	--
47	chr6:4017800-4019200	Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr6:4017800-4019200	Active TSS	Fetal Muscle Leg	muscle
49	chr6:4017800-4019200	Active TSS	Fetal Thymus	thymus
50	chr6:4017800-4019200	Active TSS	Thymus	Thymus

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