Variant report

Variant	rs9468846
Chromosome Location	chr6:30870763-30870764
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr6:30870495-30870777	K562	blood:	n/a	n/a
2	USF1	chr6:30870477-30870847	ECC-1	luminal epithelium:	n/a	chr6:30870682-30870693
3	USF2	chr6:30870525-30870886	GM12878	blood:	n/a	n/a
4	ELF1	chr6:30870452-30870853	GM12878	blood:	n/a	n/a
5	USF1	chr6:30870571-30870798	GM12878	blood:	n/a	chr6:30870682-30870693
6	PAX5	chr6:30870493-30870778	GM12878	blood:	n/a	n/a
7	MAX	chr6:30870523-30870825	GM12878	blood:	n/a	n/a
8	USF1	chr6:30870565-30870764	HepG2	liver:	n/a	chr6:30870682-30870693
9	MAX	chr6:30870615-30870775	K562	blood:	n/a	n/a
10	MAX	chr6:30870448-30870925	ECC-1	luminal epithelium:	n/a	n/a
11	MAX	chr6:30870508-30870875	K562	blood:	n/a	n/a
12	USF1	chr6:30870447-30870927	ECC-1	luminal epithelium:	n/a	chr6:30870682-30870693
13	MAX	chr6:30870455-30870972	ECC-1	luminal epithelium:	n/a	n/a
14	EBF1	chr6:30870699-30870833	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:30870158-30870831	MCF-7	breast:	n/a	n/a
16	PAX5	chr6:30870551-30870818	GM12878	blood:	n/a	n/a
17	MYC	chr6:30870603-30870765	K562	blood:	n/a	n/a
18	RUNX3	chr6:30870427-30870918	GM12878	blood:	n/a	n/a
19	MYC	chr6:30870556-30870815	K562	blood:	n/a	n/a
20	RUNX3	chr6:30870468-30870862	GM12878	blood:	n/a	n/a
21	ELF1	chr6:30870122-30870794	GM12878	blood:	n/a	n/a
22	USF1	chr6:30870554-30870822	GM12878	blood:	n/a	chr6:30870682-30870693

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30708211..30712541-chr6:30866148..30872025,6	MCF-7	breast:
2	chr6:30867554..30871649-chr6:30872522..30875092,3	MCF-7	breast:
3	chr6:30870374..30872223-chr6:30875950..30877816,2	MCF-7	breast:
4	chr6:30856055..30858937-chr6:30870726..30873383,2	MCF-7	breast:
5	chr6:30844365..30846082-chr6:30868883..30871226,2	K562	blood:
6	chr6:30865273..30868219-chr6:30870202..30872766,2	MCF-7	breast:
7	chr6:30856388..30857910-chr6:30870169..30872706,2	K562	blood:
8	chr6:30865395..30867795-chr6:30868039..30871871,4	K562	blood:
9	chr6:30861978..30864250-chr6:30870444..30872955,2	MCF-7	breast:

No data

Variant related genes	Relation type
RN7SL175P	TF binding region
ENSG00000137312	Chromatin interaction
ENSG00000213780	Chromatin interaction
ENSG00000264731	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000264594	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1049622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1049628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947111	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12206075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215246	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215409	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1419693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2074509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074511	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2074512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2229933	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239518	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2284175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2284176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2285319	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2286655	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2524236	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2894055	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213644	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3218802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218806	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3869085	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3869086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3909130	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41288539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4618569	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711247	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4711249	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4713402	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6457282	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901464	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920760	0.82[EUR][1000 genomes]
rs6921687	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6924600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743661	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756521	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295929	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295933	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9295934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9357102	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9366761	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9368646	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9378191	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9380200	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394021	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9461638	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468842	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468847	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9501032	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9501035	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9501342	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
5	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
6	nsv884109	chr6:30824532-30872203	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv1031677	chr6:30857542-30972865	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv525438	chr6:30864829-30933975	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9468846	HIST1H2BJ	cis	parietal	SCAN
rs9468846	ZKSCAN4	cis	cerebellum	SCAN
rs9468846	VARS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30854600-30875400	Weak transcription	Psoas Muscle	Psoas
2	chr6:30854800-30875200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr6:30854800-30875400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:30858400-30875400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:30858400-30875400	Weak transcription	Right Atrium	heart
6	chr6:30858400-30876000	Weak transcription	Fetal Heart	heart
7	chr6:30858600-30875200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:30858800-30875200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:30859200-30875000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:30863200-30875200	Weak transcription	Fetal Brain Male	brain
11	chr6:30863600-30875400	Weak transcription	Osteobl	bone
12	chr6:30865400-30875400	Weak transcription	HSMM	muscle
13	chr6:30865600-30875200	Weak transcription	Fetal Kidney	kidney
14	chr6:30865600-30875200	Weak transcription	Hela-S3	cervix
15	chr6:30865800-30875400	Weak transcription	NH-A	brain
16	chr6:30866400-30875200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr6:30866600-30876000	Weak transcription	Small Intestine	intestine
18	chr6:30866800-30875200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:30867200-30875200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr6:30867200-30875400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:30867200-30875400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:30867200-30875400	Weak transcription	NHLF	lung
23	chr6:30867400-30875200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:30867400-30875200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:30867400-30875200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:30867400-30875400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:30867400-30875400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:30867400-30875400	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:30867400-30875400	Weak transcription	Right Ventricle	heart
30	chr6:30867600-30873000	Weak transcription	HepG2	liver
31	chr6:30867600-30874800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:30867600-30875000	Weak transcription	Stomach Mucosa	stomach
33	chr6:30867600-30875000	Weak transcription	A549	lung
34	chr6:30867600-30875000	Weak transcription	K562	blood
35	chr6:30867600-30875200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:30867600-30875200	Weak transcription	Liver	Liver
37	chr6:30867600-30875200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:30867600-30875200	Weak transcription	Pancreas	Pancrea
39	chr6:30867600-30875200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:30867600-30875400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:30867600-30875400	Weak transcription	Adipose Nuclei	Adipose
42	chr6:30867600-30875400	Weak transcription	Aorta	Aorta
43	chr6:30867600-30875400	Weak transcription	Brain Angular Gyrus	brain
44	chr6:30867600-30875400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:30867600-30875400	Weak transcription	Brain Substantia Nigra	brain
46	chr6:30867600-30875400	Weak transcription	Fetal Lung	lung
47	chr6:30867600-30875400	Weak transcription	Left Ventricle	heart
48	chr6:30867800-30875200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:30867800-30875200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:30867800-30875200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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