Variant report

Variant	rs4870116
Chromosome Location	chr6:150244689-150244690
allele	A/C
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	MAZ	chr6:150243565-150244775	IMR90	lung:	n/a	chr6:150244690-150244700
2	RAD21	chr6:150243788-150244711	IMR90	lung:	n/a	chr6:150244161-150244171 chr6:150243810-150243822 chr6:150243811-150243824
3	E2F6	chr6:150244055-150244819	H1-hESC	embryonic stem cell:	n/a	chr6:150244326-150244335
4	MXI1	chr6:150243884-150244863	SK-N-SH	brain:	n/a	n/a
5	MAX	chr6:150243989-150244738	H1-hESC	embryonic stem cell:	n/a	chr6:150244690-150244700
6	MXI1	chr6:150244661-150244785	H1-hESC	embryonic stem cell:	n/a	n/a
7	NFIC	chr6:150244039-150244858	ECC-1	luminal epithelium:	n/a	n/a
8	MAX	chr6:150243935-150244853	ECC-1	luminal epithelium:	n/a	chr6:150244690-150244700
9	MXI1	chr6:150243746-150244842	IMR90	lung:	n/a	n/a
10	NRF1	chr6:150244133-150244853	SK-N-SH	brain:	n/a	chr6:150244386-150244397
11	ZNF263	chr6:150243623-150244829	HEK293-T-REx	kidney:	n/a	chr6:150243868-150243877
12	CTBP2	chr6:150243874-150244872	H1-hESC	embryonic stem cell:	n/a	n/a
13	RFX5	chr6:150244062-150244750	SK-N-SH	brain:	n/a	chr6:150244327-150244336
14	E2F6	chr6:150244097-150244755	H1-hESC	embryonic stem cell:	n/a	chr6:150244326-150244335
15	MAX	chr6:150243977-150244782	ECC-1	luminal epithelium:	n/a	chr6:150244690-150244700
16	NFIC	chr6:150244056-150244744	ECC-1	luminal epithelium:	n/a	n/a
17	BACH1	chr6:150244559-150244801	H1-hESC	embryonic stem cell:	n/a	n/a
18	NFIC	chr6:150244093-150244812	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:149865589..149867401-chr6:150242514..150245357,2	MCF-7	breast:
2	chr6:150217021..150219534-chr6:150242538..150245487,2	MCF-7	breast:
3	chr6:150181490..150187274-chr6:150243970..150248410,8	MCF-7	breast:

Variant related genes	Relation type
RAET1G	TF binding region
ENSG00000131013	Chromatin interaction
ENSG00000268592	Chromatin interaction
ENSG00000120256	Chromatin interaction
ENSG00000164520	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1334510	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2095376	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2342767	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2342768	0.80[EUR][1000 genomes]
rs2342769	0.92[EUR][1000 genomes]
rs2342770	0.92[EUR][1000 genomes]
rs3823021	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4242281	0.94[ASN][1000 genomes]
rs4458704	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4869763	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4869764	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4870109	0.94[ASN][1000 genomes]
rs6557133	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6933882	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6935829	0.91[EUR][1000 genomes]
rs6939761	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7740145	0.92[EUR][1000 genomes]
rs7742692	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7742993	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7744821	0.92[EUR][1000 genomes]
rs7747435	0.88[EUR][1000 genomes]
rs7747457	0.92[EUR][1000 genomes]
rs7753544	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7756850	0.91[EUR][1000 genomes]
rs7757972	0.92[EUR][1000 genomes]
rs7757984	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7758020	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7758033	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7763719	0.82[AMR][1000 genomes]
rs7763849	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7764376	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7767588	0.90[EUR][1000 genomes]
rs7767592	0.90[EUR][1000 genomes]
rs7768626	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7768665	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7769118	0.91[EUR][1000 genomes]
rs7771014	0.86[EUR][1000 genomes]
rs7774787	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9322225	0.81[EUR][1000 genomes]
rs9322228	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9371215	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9371223	0.91[EUR][1000 genomes]
rs9371504	0.83[EUR][1000 genomes]
rs9371505	0.83[EUR][1000 genomes]
rs9371533	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9371542	0.91[EUR][1000 genomes]
rs9371544	0.92[EUR][1000 genomes]
rs9383577	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9383584	0.92[EUR][1000 genomes]
rs9383912	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9383913	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9383914	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9383921	0.92[EUR][1000 genomes]
rs9383940	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9397058	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9397398	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9397420	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9397434	0.92[EUR][1000 genomes]
rs9478241	0.93[ASN][1000 genomes]
rs9968871	0.91[EUR][1000 genomes]
rs9969044	0.91[EUR][1000 genomes]
rs9986576	0.94[ASN][1000 genomes]

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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4870116	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs4870116	RAET1G	cis	Thyroid	GTEx
rs4870116	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs4870116	RP11-350J20.9	cis	Heart Left Ventricle	GTEx
rs4870116	RP11-350J20.5	cis	Thyroid	GTEx
rs4870116	RP11-350J20.9	cis	Muscle Skeletal	GTEx
rs4870116	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs4870116	RAET1G	cis	Artery Tibial	GTEx
rs4870116	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs4870116	LRP11	cis	Adipose Subcutaneous	GTEx
rs4870116	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs4870116	RAET1E	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150242800-150247800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:150243400-150244800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:150243400-150244800	Flanking Active TSS	HMEC	breast
4	chr6:150243400-150245000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:150243400-150245000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:150243600-150244800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
7	chr6:150243600-150244800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr6:150243600-150244800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:150243600-150244800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:150243600-150244800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:150243600-150244800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
12	chr6:150243600-150244800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
13	chr6:150243600-150244800	Flanking Bivalent TSS/Enh	HepG2	liver
14	chr6:150243600-150244800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
15	chr6:150243600-150245000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:150243600-150245000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:150243600-150245000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:150243800-150244800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr6:150243800-150244800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:150243800-150244800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
21	chr6:150243800-150244800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
22	chr6:150243800-150244800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:150243800-150244800	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr6:150243800-150244800	Active TSS	Aorta	Aorta
25	chr6:150243800-150244800	Flanking Active TSS	Liver	Liver
26	chr6:150243800-150244800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
27	chr6:150243800-150244800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:150243800-150244800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
29	chr6:150243800-150244800	Bivalent/Poised TSS	Fetal Kidney	kidney
30	chr6:150243800-150244800	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr6:150243800-150244800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
32	chr6:150243800-150244800	Flanking Bivalent TSS/Enh	Placenta	Placenta
33	chr6:150243800-150244800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
34	chr6:150243800-150244800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
35	chr6:150243800-150244800	Active TSS	HSMMtube	muscle
36	chr6:150243800-150244800	Flanking Active TSS	HUVEC	blood vessel
37	chr6:150243800-150245000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:150243800-150245000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
39	chr6:150243800-150245000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
40	chr6:150243800-150245000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
41	chr6:150243800-150245000	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:150243800-150245000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
43	chr6:150243800-150245000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
44	chr6:150243800-150245000	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:150243800-150245000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
46	chr6:150243800-150245000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
47	chr6:150243800-150245000	Active TSS	Right Atrium	heart
48	chr6:150244000-150244800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
49	chr6:150244000-150244800	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
50	chr6:150244000-150244800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood

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