Variant report

Variant	rs9468147
Chromosome Location	chr6:27486711-27486712
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	JUND	chr6:27486497-27487525	K562	blood:	n/a	chr6:27486575-27486589
2	MXI1	chr6:27486414-27487448	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr6:27486678-27487004	K562	blood:	n/a	n/a
4	RCOR1	chr6:27486614-27487630	Hela-S3	cervix:	n/a	n/a
5	MAFF	chr6:27486651-27486902	HepG2	liver:	n/a	n/a
6	CTCF	chr6:27486660-27486810	HEK293	kidney:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
7	CTCF	chr6:27486680-27486830	HRPEpiC	eye:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
8	RAD21	chr6:27486548-27487440	IMR90	lung:	n/a	chr6:27486743-27486762
9	CTCF	chr6:27486660-27486810	HPF	lung:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
10	TBL1XR1	chr6:27486542-27486922	K562	blood:	n/a	n/a
11	SIN3A	chr6:27486625-27487479	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAFF	chr6:27486585-27486823	K562	blood:	n/a	n/a
13	CTCF	chr6:27486609-27486914	T-47D	breast:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
14	MAZ	chr6:27486378-27487426	HepG2	liver:	n/a	n/a
15	KAP1	chr6:27486352-27487579	U2OS	brain:	n/a	n/a
16	RAD21	chr6:27486515-27486999	H1-hESC	embryonic stem cell:	n/a	chr6:27486743-27486762
17	HEY1	chr6:27486650-27487438	K562	blood:	n/a	n/a
18	STAT3	chr6:27486597-27486864	MCF10A-Er-Src	breast:	n/a	chr6:27486746-27486769 chr6:27486694-27486702
19	CTCF	chr6:27486660-27486810	NHDF-neo	bronchial:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
20	MAX	chr6:27486590-27487631	A549	lung:	n/a	n/a
21	EP300	chr6:27486626-27487490	K562	blood:	n/a	n/a
22	RAD21	chr6:27486558-27487026	HepG2	liver:	n/a	chr6:27486743-27486762
23	CTCF	chr6:27486700-27486850	Caco-2	colon:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
24	MBD4	chr6:27486242-27487452	HepG2	liver:	n/a	n/a
25	GTF2F1	chr6:27486570-27487423	K562	blood:	n/a	n/a
26	RAD21	chr6:27486487-27487005	HepG2	liver:	n/a	chr6:27486743-27486762
27	ATF3	chr6:27486563-27487594	HCT-116	colon:	n/a	n/a
28	CTCF	chr6:27486660-27486810	GM12864	blood:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
29	MYBL2	chr6:27486479-27487671	HepG2	liver:	n/a	n/a
30	CTCF	chr6:27486689-27487089	GM19238	blood:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
31	RAD21	chr6:27486495-27487121	MCF-7	breast:	n/a	chr6:27486743-27486762
32	CTCF	chr6:27486629-27486816	SK-N-SH_RA	brain:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
33	NR2F2	chr6:27486116-27487695	K562	blood:	n/a	n/a
34	MAX	chr6:27486651-27487348	K562	blood:	n/a	n/a
35	CTCF	chr6:27486529-27487431	IMR90	lung:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
36	CTCF	chr6:27486660-27486810	HMF	breast:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
37	CTCF	chr6:27486660-27486810	HVMF	connective:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
38	CTCF	chr6:27486680-27486830	GM12868	blood:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
39	CTCF	chr6:27486607-27486863	A549	lung:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
40	RAD21	chr6:27486587-27486974	GM12878	blood:	n/a	chr6:27486743-27486762
41	CTCF	chr6:27486660-27486810	AG09319	gingival:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
42	CBX3	chr6:27486206-27487598	K562	blood:	n/a	n/a
43	YY1	chr6:27486486-27486792	SK-N-SH_RA	brain:	n/a	n/a
44	CTCF	chr6:27486700-27486850	GM12873	blood:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
45	CTCF	chr6:27486660-27486810	GM12873	blood:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
46	CEBPB	chr6:27486533-27487491	Hela-S3	cervix:	n/a	n/a
47	STAT5A	chr6:27486495-27487538	GM12878	blood:	n/a	chr6:27486746-27486769 chr6:27486694-27486702
48	CTCF	chr6:27486664-27486853	GM20000	blood:	n/a	chr6:27486745-27486758 chr6:27486742-27486760
49	MAX	chr6:27486126-27487473	NB4	blood:	n/a	n/a
50	CEBPB	chr6:27486497-27487539	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:27484584..27488332-chr6:27510718..27517448,9	K562	blood:
2	chr6:27486617..27489499-chr6:27758856..27760750,2	K562	blood:
3	chr6:27485761..27488358-chr6:27559045..27561077,2	K562	blood:
4	chr6:27475135..27475691-chr6:27486008..27486713,2	K562	blood:
5	chr6:27485174..27486932-chr6:27777481..27778994,2	K562	blood:
6	chr6:27472071..27474860-chr6:27486354..27488722,3	K562	blood:
7	chr6:27485746..27487323-chr6:27576399..27577877,8	MCF-7	breast:
8	chr6:27485668..27488646-chr6:27758590..27761132,3	K562	blood:
9	chr6:27484707..27486916-chr6:27761947..27763792,2	MCF-7	breast:
10	chr6:27484573..27488622-chr6:27496646..27500202,4	K562	blood:
11	chr6:27469947..27474974-chr6:27485508..27488698,9	K562	blood:
12	chr6:26029984..26031821-chr6:27485687..27487793,2	K562	blood:
13	chr6:27483867..27487300-chr6:27514460..27517448,4	K562	blood:
14	chr6:27486493..27487200-chr6:27719731..27720643,4	K562	blood:
15	chr6:27486324..27487326-chr6:27576697..27577724,6	K562	blood:
16	chr6:27485493..27487721-chr6:27575834..27578755,2	MCF-7	breast:
17	chr6:27484948..27487282-chr6:27561197..27562747,2	K562	blood:
18	chr6:27486558..27487262-chr6:27654877..27655530,2	MCF-7	breast:
19	chr6:27485174..27486932-chr6:27777273..27778994,3	K562	blood:
20	chr6:27485284..27487587-chr6:27859462..27861025,2	K562	blood:

Variant related genes	Relation type
ENSG00000270666	TF binding region
HNRNPA1P1	TF binding region
ENSG00000233224	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000203813	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1010261	0.81[YRI][hapmap]
rs16867901	0.90[YRI][hapmap]
rs16867911	0.81[YRI][hapmap]
rs4616979	1.00[AMR][1000 genomes]
rs56816292	0.86[ASN][1000 genomes]
rs73395377	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73395381	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73395396	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9295739	0.90[YRI][hapmap]
rs9468058	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9468160	0.90[YRI][hapmap]
rs9468189	0.87[YRI][hapmap]
rs9468190	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv462665	chr6:27458013-27547792	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv601203	chr6:27458013-27547792	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv1017347	chr6:27483816-27605842	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9468147	Hs.158943	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27485800-27487400	Active TSS	Right Atrium	heart
2	chr6:27486000-27486800	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr6:27486000-27487000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr6:27486000-27487000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:27486000-27487400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr6:27486000-27487400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:27486000-27487400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:27486000-27487400	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
9	chr6:27486000-27487400	Active TSS	Right Ventricle	heart
10	chr6:27486000-27487400	Active TSS	HSMMtube	muscle
11	chr6:27486000-27487400	Active TSS	NHLF	lung
12	chr6:27486000-27487600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:27486000-27487600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:27486000-27487600	Active TSS	Aorta	Aorta
15	chr6:27486000-27487800	Active TSS	A549	lung
16	chr6:27486200-27486800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:27486200-27486800	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr6:27486200-27486800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr6:27486200-27487200	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr6:27486200-27487200	Flanking Active TSS	Liver	Liver
21	chr6:27486200-27487200	Active TSS	Esophagus	oesophagus
22	chr6:27486200-27487400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:27486200-27487400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:27486200-27487400	Active TSS	Colonic Mucosa	Colon
25	chr6:27486200-27487400	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr6:27486200-27487400	Active TSS	Pancreas	Pancrea
27	chr6:27486200-27487400	Active TSS	NH-A	brain
28	chr6:27486200-27487600	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr6:27486200-27487600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr6:27486200-27487600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:27486200-27487600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:27486200-27487600	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr6:27486200-27487600	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr6:27486200-27487600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:27486200-27487600	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr6:27486200-27487600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
37	chr6:27486200-27487600	Active TSS	Ovary	ovary
38	chr6:27486200-27487800	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr6:27486200-27487800	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr6:27486200-27487800	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr6:27486400-27486800	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr6:27486400-27486800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:27486400-27487200	Active TSS	Lung	lung
44	chr6:27486400-27487400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr6:27486400-27487400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:27486400-27487400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:27486400-27487400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:27486400-27487400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:27486400-27487400	Active TSS	Fetal Intestine Large	intestine
50	chr6:27486400-27487400	Bivalent/Poised TSS	Fetal Kidney	kidney

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