Variant report

Variant	rs9405693
Chromosome Location	chr6:4021238-4021239
allele	A/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	POLR2A	chr6:4020913-4022072	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr6:4021137-4022263	GM12892	blood:	n/a	n/a
3	POLR2A	chr6:4021193-4022278	HepG2	liver:	n/a	n/a
4	TEAD4	chr6:4021078-4021727	K562	blood:	n/a	n/a
5	BHLHE40	chr6:4021012-4022324	GM12878	blood:	n/a	chr6:4021905-4021921 chr6:4021972-4021988
6	POLR2A	chr6:4021173-4022311	GM15510	blood:	n/a	n/a
7	MAX	chr6:4021000-4022373	HCT-116	colon:	n/a	n/a
8	TAF1	chr6:4021233-4021867	SK-N-SH	brain:	n/a	n/a
9	CREB1	chr6:4021233-4022097	H1-hESC	embryonic stem cell:	n/a	n/a
10	MYBL2	chr6:4020900-4022360	HepG2	liver:	n/a	n/a
11	MYC	chr6:4021205-4022302	NB4	blood:	n/a	n/a
12	POLR2A	chr6:4021052-4022361	GM12892	blood:	n/a	n/a
13	NRF1	chr6:4021228-4021726	Hela-S3	cervix:	n/a	chr6:4021559-4021570
14	YY1	chr6:4021210-4022118	K562	blood:	n/a	chr6:4021979-4021990 chr6:4021655-4021667
15	JUND	chr6:4021222-4021807	HepG2	liver:	n/a	n/a
16	POLR2A	chr6:4021060-4021969	ProgFib	skin:	n/a	n/a
17	POLR2A	chr6:4021051-4022249	HL-60	blood:	n/a	n/a
18	ATF1	chr6:4021218-4021708	K562	blood:	n/a	n/a
19	YY1	chr6:4021147-4022327	GM12878	blood:	n/a	chr6:4021979-4021990 chr6:4021655-4021667
20	MAX	chr6:4021119-4022315	MCF-7	breast:	n/a	n/a
21	TAF1	chr6:4021205-4022255	H1-hESC	embryonic stem cell:	n/a	n/a
22	MXI1	chr6:4020932-4022924	IMR90	lung:	n/a	n/a
23	POLR2A	chr6:4021195-4022353	IMR90	lung:	n/a	n/a
24	NFIC	chr6:4021148-4021987	GM12878	blood:	n/a	n/a
25	MYC	chr6:4020304-4022486	K562	blood:	n/a	n/a
26	POLR2A	chr6:4021136-4022245	GM12891	blood:	n/a	n/a
27	TBP	chr6:4020951-4022393	K562	blood:	n/a	n/a
28	POLR2A	chr6:4021146-4021968	U87	brain:	n/a	n/a
29	YY1	chr6:4021192-4022167	K562	blood:	n/a	chr6:4021979-4021990 chr6:4021655-4021667
30	TAF1	chr6:4021111-4022336	ECC-1	luminal epithelium:	n/a	n/a
31	MAX	chr6:4021136-4022097	A549	lung:	n/a	n/a
32	ETS1	chr6:4021225-4022177	K562	blood:	n/a	chr6:4021935-4021948
33	POLR2A	chr6:4021134-4021938	HUVEC	blood vessel:	n/a	n/a
34	TBP	chr6:4021050-4022647	HepG2	liver:	n/a	n/a
35	ELF1	chr6:4021189-4022116	HepG2	liver:	n/a	chr6:4021457-4021466
36	YY1	chr6:4021035-4022669	SK-N-SH	brain:	n/a	chr6:4021979-4021990 chr6:4021655-4021667
37	POLR2A	chr6:4021205-4021814	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr6:4021141-4022429	GM12878	blood:	n/a	n/a
39	MAX	chr6:4021135-4022319	MCF-7	breast:	n/a	n/a
40	NR2F2	chr6:4021129-4022140	MCF-7	breast:	n/a	n/a
41	POLR2A	chr6:4021091-4022405	GM12878	blood:	n/a	n/a
42	EGR1	chr6:4021219-4021741	K562	blood:	n/a	n/a
43	GTF2B	chr6:4021176-4021782	K562	blood:	n/a	n/a
44	POLR2A	chr6:4020325-4022372	K562	blood:	n/a	n/a
45	MAX	chr6:4021158-4022313	ECC-1	luminal epithelium:	n/a	n/a
46	STAT5A	chr6:4021061-4022137	K562	blood:	n/a	n/a
47	FOXM1	chr6:4021205-4022000	GM12878	blood:	n/a	n/a
48	NR2F2	chr6:4021115-4022019	K562	blood:	n/a	n/a
49	ZNF143	chr6:4020991-4022320	GM12878	blood:	n/a	n/a
50	POU2F2	chr6:4021214-4022295	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:4016355..4024618-chr6:4131840..4138381,21	K562	blood:
2	chr6:4017302..4025509-chr6:4131840..4138381,19	K562	blood:
3	chr6:4019656..4024130-chr6:4049502..4053557,5	K562	blood:
4	chr6:4016030..4019961-chr6:4020836..4023596,5	MCF-7	breast:
5	chr6:3064193..3067093-chr6:4018828..4021333,2	K562	blood:
6	chr6:4020118..4022120-chr6:4056131..4059470,3	K562	blood:
7	chr17:39844666..39845562-chr6:4020847..4021646,2	Hela-S3	cervix:
8	chr6:4020118..4023028-chr6:4056131..4059224,3	K562	blood:

Variant related genes	Relation type
PRPF4B	TF binding region
ENSG00000234817	Chromatin interaction
ENSG00000145975	Chromatin interaction
ENSG00000198721	Chromatin interaction
ENSG00000254821	Chromatin interaction
ENSG00000112739	Chromatin interaction
ENSG00000173812	Chromatin interaction
ENSG00000137275	Chromatin interaction
ENSG00000272248	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11759303	0.82[CHB][hapmap]
rs12195138	0.82[ASN][1000 genomes]
rs12198921	0.84[JPT][hapmap]
rs1543355	0.91[CEU][hapmap]
rs1969836	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1969837	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2745451	0.87[CEU][hapmap]
rs2745452	0.88[CEU][hapmap]
rs3747761	0.83[EUR][1000 genomes]
rs3747762	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs3747763	0.82[EUR][1000 genomes]
rs57139617	0.82[ASN][1000 genomes]
rs6906467	0.91[CEU][hapmap]
rs6914776	0.81[JPT][hapmap]
rs6941706	0.83[EUR][1000 genomes]
rs697745	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs707980	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs707981	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs707982	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs707983	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs707984	0.83[EUR][1000 genomes]
rs707985	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs707987	0.82[EUR][1000 genomes]
rs707988	0.82[EUR][1000 genomes]
rs7763233	0.82[EUR][1000 genomes]
rs853396	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs853399	0.82[EUR][1000 genomes]
rs853400	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs853403	0.91[CEU][hapmap]
rs853404	0.82[EUR][1000 genomes]
rs853405	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs853406	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs853407	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs853408	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs853411	0.87[CEU][hapmap]
rs860477	0.82[EUR][1000 genomes]
rs860478	0.81[EUR][1000 genomes]
rs9328215	0.86[CEU][hapmap]
rs9328216	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs9392546	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9392547	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9392548	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9405217	0.88[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs942473	0.81[ASN][1000 genomes]
rs9503893	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv2370815	chr6:4020815-4021256	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 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	chr6:4017400-4023000	Active TSS	K562	blood
2	chr6:4019600-4023000	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr6:4020000-4023000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr6:4020000-4023200	Active TSS	HSMM	muscle
5	chr6:4020000-4023400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:4020200-4022800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:4020400-4021400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr6:4020600-4021400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:4020600-4021400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:4020600-4021800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:4020600-4022800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:4020800-4021400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:4020800-4021400	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr6:4020800-4021400	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr6:4020800-4021400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr6:4020800-4021400	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr6:4020800-4021400	Flanking Active TSS	Liver	Liver
18	chr6:4020800-4021400	Flanking Active TSS	Brain Substantia Nigra	brain
19	chr6:4020800-4021400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr6:4020800-4021400	Flanking Active TSS	HUVEC	blood vessel
21	chr6:4020800-4021400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr6:4020800-4022400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr6:4020800-4022600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr6:4020800-4022600	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr6:4020800-4022600	Active TSS	Fetal Kidney	kidney
26	chr6:4020800-4022600	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr6:4020800-4022800	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr6:4020800-4022800	Active TSS	NHLF	lung
29	chr6:4020800-4022800	Active TSS	Osteobl	bone
30	chr6:4020800-4023000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:4020800-4023000	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr6:4020800-4023000	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr6:4020800-4023000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:4020800-4023000	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr6:4020800-4023000	Active TSS	NH-A	brain
36	chr6:4020800-4023000	Active TSS	NHEK	skin
37	chr6:4020800-4023200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:4020800-4023200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:4020800-4023200	Active TSS	Colonic Mucosa	Colon
40	chr6:4020800-4023200	Active TSS	Right Ventricle	heart
41	chr6:4020800-4023200	Active TSS	NHDF-Ad	bronchial
42	chr6:4020800-4023400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:4020800-4023600	Active TSS	Psoas Muscle	Psoas
44	chr6:4020800-4023600	Active TSS	Thymus	Thymus
45	chr6:4020800-4023600	Active TSS	A549	lung
46	chr6:4020800-4024000	Active TSS	HMEC	breast
47	chr6:4021000-4021400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr6:4021000-4021400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr6:4021000-4021400	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr6:4021000-4021400	Flanking Active TSS	Primary T cells from cord blood	blood

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