Variant report

Variant	rs3129975
Chromosome Location	chr6:30732054-30732055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:168)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:168 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr6:30731915-30732454	K562	blood:	n/a	n/a
2	POLR2A	chr6:30730914-30732454	HepG2	liver:	n/a	n/a
3	EP300	chr6:30731775-30732362	A549	lung:	n/a	n/a
4	CTCF	chr6:30732040-30732190	AG10803	skin:	n/a	n/a
5	POLR2A	chr6:30731138-30732437	HepG2	liver:	n/a	n/a
6	FOXA2	chr6:30731812-30732410	A549	lung:	n/a	n/a
7	POLR2A	chr6:30731278-30732399	HepG2	liver:	n/a	n/a
8	ESR1	chr6:30731776-30732376	ECC-1	luminal epithelium:	n/a	n/a
9	HEY1	chr6:30730837-30732569	HepG2	liver:	n/a	chr6:30731925-30731940
10	TAF1	chr6:30731919-30732284	PFSK-1	brain:	n/a	n/a
11	RAD21	chr6:30731249-30732374	HepG2	liver:	n/a	n/a
12	SMC3	chr6:30732007-30732357	Hela-S3	cervix:	n/a	n/a
13	FOXA1	chr6:30731757-30732384	HepG2	liver:	n/a	n/a
14	MBD4	chr6:30730857-30732447	HepG2	liver:	n/a	n/a
15	PBX3	chr6:30731344-30732357	SK-N-SH	brain:	n/a	n/a
16	MYC	chr6:30732028-30732295	K562	blood:	n/a	n/a
17	FOXA2	chr6:30731818-30732387	A549	lung:	n/a	n/a
18	HNF4A	chr6:30731265-30732341	HepG2	liver:	n/a	chr6:30731601-30731616
19	RAD21	chr6:30732000-30732376	Hela-S3	cervix:	n/a	n/a
20	CTCF	chr6:30732047-30732280	K562	blood:	n/a	n/a
21	RAD21	chr6:30731806-30732386	ECC-1	luminal epithelium:	n/a	n/a
22	CTCF	chr6:30732040-30732190	Caco-2	colon:	n/a	n/a
23	FOXA1	chr6:30731076-30732455	HepG2	liver:	n/a	n/a
24	GATA2	chr6:30731980-30732430	K562	blood:	n/a	chr6:30732034-30732041
25	REST	chr6:30731223-30732382	HepG2	liver:	n/a	n/a
26	FOSL2	chr6:30731180-30732469	HepG2	liver:	n/a	n/a
27	POLR2A	chr6:30731999-30732359	HCT-116	colon:	n/a	n/a
28	CTCF	chr6:30732040-30732190	A549	lung:	n/a	n/a
29	MAX	chr6:30731751-30732393	K562	blood:	n/a	n/a
30	HDAC2	chr6:30731900-30732468	HepG2	liver:	n/a	n/a
31	SP1	chr6:30731206-30732449	A549	lung:	n/a	n/a
32	CTCF	chr6:30732009-30732334	K562	blood:	n/a	n/a
33	KAP1	chr6:30731322-30732318	HEK293	kidney:	n/a	n/a
34	TEAD4	chr6:30731611-30732414	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr6:30731401-30732396	HUVEC	blood vessel:	n/a	n/a
36	CEBPD	chr6:30731299-30732337	HepG2	liver:	n/a	n/a
37	TEAD4	chr6:30731965-30732351	H1-hESC	embryonic stem cell:	n/a	n/a
38	TEAD4	chr6:30731937-30732355	HepG2	liver:	n/a	n/a
39	MAZ	chr6:30731119-30732346	HepG2	liver:	n/a	n/a
40	POLR2A	chr6:30731176-30732362	HepG2	liver:	n/a	n/a
41	EP300	chr6:30731906-30732330	SK-N-SH_RA	brain:	n/a	n/a
42	MAFK	chr6:30731386-30732333	HepG2	liver:	n/a	n/a
43	CTCF	chr6:30732040-30732190	HEEpiC	esophagus:	n/a	n/a
44	RAD21	chr6:30731201-30732457	HepG2	liver:	n/a	n/a
45	GATA3	chr6:30731899-30732495	A549	lung:	n/a	chr6:30732034-30732041
46	CTCF	chr6:30732020-30732170	HRPEpiC	eye:	n/a	n/a
47	SP1	chr6:30731763-30732455	A549	lung:	n/a	n/a
48	CTCF	chr6:30732040-30732190	MCF-7	breast:	n/a	n/a
49	RCOR1	chr6:30732039-30732390	K562	blood:	n/a	n/a
50	HNF4A	chr6:30731931-30732434	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30731319..30733794-chr6:30880499..30882436,2	K562	blood:
2	chr6:30688991..30691146-chr6:30731072..30732705,2	K562	blood:
3	chr6:30716396..30719291-chr6:30729856..30732825,2	K562	blood:
4	chr6:30731381..30733806-chr6:30851379..30853167,2	MCF-7	breast:
5	chr6:30731147..30732913-chr6:30849993..30851974,2	MCF-7	breast:

No data

Variant related genes	Relation type
HCG20	TF binding region
ENSG00000263608	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000204580	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11751309	0.82[ASN][1000 genomes]
rs11751330	0.82[ASN][1000 genomes]
rs11753799	0.82[ASN][1000 genomes]
rs11962021	0.82[ASN][1000 genomes]
rs3094112	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3094119	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094120	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094121	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131035	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131037	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131038	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131056	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4711231	0.80[ASN][1000 genomes]
rs9262172	0.85[EUR][1000 genomes]
rs9262173	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9262201	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
6	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
8	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
9	nsv884101	chr6:30695920-30733121	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	163 gene(s)	inside rSNPs	diseases
10	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
11	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
12	nsv870418	chr6:30713196-30755668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv527226	chr6:30716719-30772378	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
14	nsv884103	chr6:30729487-30755668	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3129975	HIST1H3J	cis	parietal	SCAN
rs3129975	HIST1H2AM	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30720600-30736600	Weak transcription	Gastric	stomach
2	chr6:30726800-30739000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:30728000-30732800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:30728000-30737000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:30728200-30736400	Weak transcription	Lung	lung
6	chr6:30728200-30736600	Weak transcription	Aorta	Aorta
7	chr6:30730400-30732200	Enhancers	Placenta Amnion	Placenta Amnion
8	chr6:30731000-30732200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:30731000-30732200	Enhancers	Fetal Kidney	kidney
10	chr6:30731000-30732200	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr6:30731000-30732200	Enhancers	GM12878-XiMat	blood
12	chr6:30731000-30732400	Enhancers	H1 Cell Line	embryonic stem cell
13	chr6:30731000-30732400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr6:30731000-30732400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr6:30731000-30732400	Enhancers	Colon Smooth Muscle	Colon
16	chr6:30731000-30732400	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr6:30731000-30732400	Flanking Active TSS	A549	lung
18	chr6:30731000-30732400	Flanking Active TSS	HepG2	liver
19	chr6:30731000-30732600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr6:30731000-30732600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:30731000-30732600	Enhancers	Fetal Heart	heart
22	chr6:30731000-30732600	Enhancers	Fetal Intestine Large	intestine
23	chr6:30731000-30732600	Enhancers	Fetal Intestine Small	intestine
24	chr6:30731000-30734600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:30731000-30735600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:30731000-30738800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:30731200-30732200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:30731200-30732200	Enhancers	H9 Cell Line	embryonic stem cell
29	chr6:30731200-30732200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr6:30731200-30732200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr6:30731200-30732200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:30731200-30732200	Enhancers	Right Ventricle	heart
33	chr6:30731200-30732400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr6:30731200-30732400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:30731200-30732400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:30731200-30732400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr6:30731200-30732400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:30731200-30732400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:30731200-30732400	Enhancers	Fetal Stomach	stomach
40	chr6:30731200-30732400	Enhancers	Fetal Thymus	thymus
41	chr6:30731200-30732400	Enhancers	Rectal Smooth Muscle	rectum
42	chr6:30731200-30732400	Enhancers	Stomach Mucosa	stomach
43	chr6:30731200-30732400	Enhancers	Dnd41	blood
44	chr6:30731200-30732400	Enhancers	HMEC	breast
45	chr6:30731200-30732400	Enhancers	HSMMtube	muscle
46	chr6:30731200-30732400	Enhancers	K562	blood
47	chr6:30731200-30732400	Enhancers	NH-A	brain
48	chr6:30731200-30732600	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr6:30731200-30732800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:30731200-30732800	Enhancers	Placenta	Placenta

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