Variant report

Variant	rs4330675
Chromosome Location	chr8:125488907-125488908
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	HCFC1	chr8:125485176-125489186	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr8:125488436-125488980	HepG2	liver:	n/a	n/a
3	REST	chr8:125486009-125488915	H1-neurons	neurons:	n/a	chr8:125487587-125487597
4	CHD1	chr8:125486196-125489079	GM12878	blood:	n/a	n/a
5	KAP1	chr8:125487387-125489041	HEK293	kidney:	n/a	n/a
6	JUN	chr8:125486154-125489145	K562	blood:	n/a	chr8:125486890-125486903 chr8:125487589-125487598
7	EP300	chr8:125488472-125488997	K562	blood:	n/a	n/a
8	CTCF	chr8:125488840-125488990	HMEC	breast:	n/a	n/a
9	POLR2A	chr8:125485914-125489028	GM12891	blood:	n/a	n/a
10	WRNIP1	chr8:125488338-125489056	GM12878	blood:	n/a	n/a
11	BHLHE40	chr8:125488522-125488999	K562	blood:	n/a	n/a
12	MAFK	chr8:125485930-125490370	GM12878	blood:	n/a	chr8:125489996-125490007 chr8:125489995-125490006 chr8:125490001-125490017 chr8:125489998-125490014 chr8:125490004-125490018 chr8:125489996-125490016 chr8:125489995-125490010 chr8:125489995-125490006 chr8:125489999-125490013
13	POLR2A	chr8:125485210-125488989	MCF10A-Er-Src	breast:	n/a	n/a
14	CTCF	chr8:125486481-125489047	A549	lung:	n/a	chr8:125486829-125486842
15	CTCF	chr8:125488840-125488990	HVMF	connective:	n/a	n/a
16	RCOR1	chr8:125488231-125488924	GM12878	blood:	n/a	n/a
17	CCNT2	chr8:125488362-125488996	K562	blood:	n/a	n/a
18	GATA3	chr8:125488849-125489316	T-47D	breast:	n/a	chr8:125489147-125489154
19	POLR2A	chr8:125485912-125489246	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr8:125485202-125488998	PBDE	blood:	n/a	n/a
21	NR2F2	chr8:125488274-125489008	K562	blood:	n/a	n/a
22	NR2F2	chr8:125488213-125489144	MCF-7	breast:	n/a	n/a
23	ELF1	chr8:125488238-125489252	MCF-7	breast:	n/a	chr8:125488628-125488641
24	POLR2A	chr8:125488899-125488965	MCF-7	breast:	n/a	n/a
25	TBL1XR1	chr8:125488050-125489216	K562	blood:	n/a	n/a
26	SIN3A	chr8:125486410-125489001	GM12878	blood:	n/a	n/a
27	CTCF	chr8:125488860-125489010	WI-38	lung:	n/a	n/a
28	NR2F2	chr8:125488286-125489102	MCF-7	breast:	n/a	n/a
29	CTCF	chr8:125488370-125488909	IMR90	lung:	n/a	n/a
30	KAP1	chr8:125488341-125489128	U2OS	brain:	n/a	n/a
31	ELF1	chr8:125488386-125488945	GM12878	blood:	n/a	chr8:125488628-125488641
32	USF2	chr8:125488772-125489055	K562	blood:	n/a	n/a
33	NR2F2	chr8:125488120-125489035	K562	blood:	n/a	n/a
34	POLR2A	chr8:125478436-125489342	K562	blood:	n/a	n/a
35	CTCF	chr8:125488800-125488950	AoAF	blood vessel:	n/a	n/a
36	CTCF	chr8:125488347-125488933	MCF-7	breast:	n/a	n/a
37	MAZ	chr8:125485791-125488965	IMR90	lung:	n/a	chr8:125488265-125488274 chr8:125487056-125487066 chr8:125486876-125486885 chr8:125487912-125487921
38	EBF1	chr8:125488136-125489224	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:125482386..125490832-chr8:125532319..125553620,55	MCF-7	breast:
2	chr8:125487371..125489055-chr8:125515121..125516817,2	MCF-7	breast:
3	chr8:125488240..125490491-chr8:125514107..125516385,2	MCF-7	breast:
4	chr8:125484053..125491713-chr8:125548138..125554442,21	K562	blood:
5	chr8:125487680..125490631-chr8:125553393..125557041,3	MCF-7	breast:
6	chr8:124818284..124820707-chr8:125487320..125489749,2	K562	blood:
7	chr8:125485971..125490407-chr8:125553790..125556730,4	MCF-7	breast:
8	chr8:125484651..125489587-chr8:125535041..125543731,11	K562	blood:
9	chr8:125459763..125466513-chr8:125482159..125488968,22	K562	blood:
10	chr8:125483604..125491110-chr8:125548591..125554086,23	K562	blood:
11	chr8:125488174..125490894-chr8:126019892..126022502,2	K562	blood:
12	chr8:125487117..125490518-chr8:125542261..125547751,5	K562	blood:
13	chr8:125487104..125489610-chr8:126009410..126011098,2	MCF-7	breast:
14	chr8:125487492..125489974-chr8:125525285..125527024,3	K562	blood:
15	chr8:125484298..125489708-chr8:125549185..125553061,9	MCF-7	breast:
16	chr8:125485755..125491202-chr8:125535208..125540184,8	MCF-7	breast:
17	chr8:125458285..125469406-chr8:125482519..125490004,41	MCF-7	breast:

Variant related genes	Relation type
RNF139-AS1	TF binding region
ENSG00000147684	Chromatin interaction
ENSG00000253513	Chromatin interaction
ENSG00000183665	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000104549	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10195	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10956186	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13253319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[ASN][1000 genomes]
rs16899643	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16899656	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16899660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16899663	0.87[YRI][hapmap]
rs17298171	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs3812470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812473	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3829033	0.89[CEU][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3829037	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[ASN][1000 genomes]
rs4527852	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4613980	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4621790	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57929284	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6981043	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6989097	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6997089	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7017148	0.88[ASN][1000 genomes]
rs71516748	0.97[ASN][1000 genomes]
rs72713019	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72713023	0.85[EUR][1000 genomes]
rs72713032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72713042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72713045	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72713053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72713055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713059	0.86[EUR][1000 genomes]
rs72713071	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713073	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713075	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713077	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713084	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713096	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72713098	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72714708	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73704274	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9643197	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][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	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv1017848	chr8:125432689-125489052	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
3	nsv891433	chr8:125438093-125498547	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125484000-125489000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr8:125484200-125489200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr8:125484200-125489400	Active TSS	K562	blood
4	chr8:125484400-125489000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr8:125484400-125489600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr8:125484600-125489200	Active TSS	Right Ventricle	heart
7	chr8:125484800-125489000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr8:125484800-125489200	Active TSS	Aorta	Aorta
9	chr8:125484800-125489200	Active TSS	Ovary	ovary
10	chr8:125484800-125489200	Active TSS	A549	lung
11	chr8:125484800-125489400	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr8:125484800-125489400	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr8:125484800-125489400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr8:125484800-125490200	Active TSS	GM12878-XiMat	blood
15	chr8:125485200-125489000	Active TSS	Fetal Muscle Trunk	muscle
16	chr8:125485200-125489200	Active TSS	H1 Cell Line	embryonic stem cell
17	chr8:125485600-125489200	Active TSS	Psoas Muscle	Psoas
18	chr8:125485800-125489000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr8:125485800-125489000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr8:125486200-125489400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr8:125487400-125489400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr8:125487400-125489400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr8:125487600-125489000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr8:125487600-125489200	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr8:125487600-125489200	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr8:125487600-125489600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr8:125487800-125489000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr8:125487800-125489000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr8:125487800-125489000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr8:125487800-125489200	Flanking Active TSS	Liver	Liver
31	chr8:125487800-125489200	Active TSS	Right Atrium	heart
32	chr8:125487800-125489400	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr8:125487800-125489400	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr8:125487800-125489600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr8:125488000-125489000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr8:125488000-125489000	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr8:125488000-125489200	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr8:125488000-125489200	Enhancers	Placenta Amnion	Placenta Amnion
39	chr8:125488000-125489400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr8:125488000-125489400	Flanking Active TSS	HUVEC	blood vessel
41	chr8:125488000-125489400	Flanking Active TSS	Osteobl	bone
42	chr8:125488000-125489600	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr8:125488000-125489600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr8:125488000-125490200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr8:125488000-125503400	Weak transcription	Spleen	Spleen
46	chr8:125488200-125489200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr8:125488200-125489200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr8:125488200-125489200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr8:125488200-125489200	Flanking Active TSS	Fetal Lung	lung
50	chr8:125488200-125489400	Flanking Active TSS	Fetal Brain Female	brain

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