Variant report

Variant	rs9371504
Chromosome Location	chr6:150184080-150184081
allele	A/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	POLR2A	chr6:150181876-150186422	IMR90	lung:	n/a	n/a
2	RAD21	chr6:150183910-150186688	SK-N-SH	brain:	n/a	chr6:150184360-150184374 chr6:150185705-150185718 chr6:150185250-150185264
3	CEBPB	chr6:150184008-150185779	Hela-S3	cervix:	n/a	chr6:150184098-150184115
4	STAT3	chr6:150184070-150184539	MCF10A-Er-Src	breast:	n/a	chr6:150184284-150184291 chr6:150184284-150184298
5	POLR2A	chr6:150183914-150185821	MCF10A-Er-Src	breast:	n/a	n/a
6	TCF7L2	chr6:150183911-150185124	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr6:150183904-150186614	SK-N-SH	brain:	n/a	n/a
8	CHD1	chr6:150181747-150185902	IMR90	lung:	n/a	chr6:150185305-150185315
9	MAX	chr6:150184053-150185754	Hela-S3	cervix:	n/a	chr6:150185270-150185280
10	MXI1	chr6:150184000-150186450	IMR90	lung:	n/a	n/a
11	STAT3	chr6:150184015-150184526	MCF10A-Er-Src	breast:	n/a	chr6:150184284-150184291 chr6:150184284-150184298
12	MAX	chr6:150184054-150186471	A549	lung:	n/a	chr6:150185270-150185280
13	POLR2A	chr6:150181811-150186475	MCF10A-Er-Src	breast:	n/a	n/a
14	HA-E2F1	chr6:150184075-150185803	MCF-7	breast:	n/a	chr6:150185587-150185597 chr6:150184350-150184359
15	POLR2A	chr6:150184016-150185945	Hela-S3	cervix:	n/a	n/a
16	MAZ	chr6:150183983-150186584	IMR90	lung:	n/a	chr6:150185270-150185280
17	CTCF	chr6:150184074-150186891	SK-N-SH	brain:	n/a	chr6:150185422-150185435
18	SMC3	chr6:150183916-150186608	SK-N-SH	brain:	n/a	chr6:150185239-150185249
19	REST	chr6:150183977-150186692	H1-neurons	neurons:	n/a	chr6:150185423-150185436 chr6:150185591-150185604 chr6:150185692-150185705
20	EGR1	chr6:150183992-150184284	K562	blood:	n/a	chr6:150184147-150184162
21	EGR1	chr6:150184002-150184318	K562	blood:	n/a	chr6:150184147-150184162
22	POLR2A	chr6:150184042-150185866	HepG2	liver:	n/a	n/a
23	STAT3	chr6:150184070-150184379	MCF10A-Er-Src	breast:	n/a	chr6:150184284-150184291 chr6:150184284-150184298
24	CEBPB	chr6:150183995-150184329	IMR90	lung:	n/a	chr6:150184098-150184115

No.	Distal block	Cell Line	Cell type
1	chr6:150183161..150188305-chr6:150206346..150214162,9	MCF-7	breast:
2	chr6:150037075..150038991-chr6:150181496..150184249,2	K562	blood:
3	chr6:150181490..150187274-chr6:150243970..150248410,8	MCF-7	breast:
4	chr6:150183832..150186232-chr6:150215270..150224001,9	MCF-7	breast:
5	chr6:150036146..150038991-chr6:150182749..150185016,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAET1E-2	chr6:150184027-150184273	expReg_chr6_11262_-

Variant related genes	Relation type
ENSG00000268592	TF binding region
ENSG00000223701	Chromatin interaction
ENSG00000203722	Chromatin interaction
ENSG00000164520	Chromatin interaction
ENSG00000131023	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1334510	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1889471	0.86[EUR][1000 genomes]
rs2095376	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2342767	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2342769	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2342770	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3823021	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4458704	0.85[EUR][1000 genomes]
rs4869763	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4869764	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4870116	0.83[EUR][1000 genomes]
rs6557133	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6933882	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6935829	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6939761	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7740145	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7742692	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7742993	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7744821	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7747435	0.85[EUR][1000 genomes]
rs7747457	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7753544	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7756850	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7757972	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7757984	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7758020	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7758033	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7763719	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7763849	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7764376	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7767588	0.88[EUR][1000 genomes]
rs7767592	0.88[EUR][1000 genomes]
rs7768626	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7768665	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7769118	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7771014	0.86[EUR][1000 genomes]
rs7774787	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9322225	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9322228	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9371215	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9371223	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9371505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9371533	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9371542	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9371544	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9383577	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9383584	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9383912	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9383913	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9383914	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9383921	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9383940	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9397058	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9397398	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9397420	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9397434	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9478192	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9968871	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9969044	0.81[AMR][1000 genomes];0.90[EUR][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	esv3437961	chr6:150182459-150187257	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv823860	chr6:150183482-150186226	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs9371504	RP11-350J20.9	cis	Muscle Skeletal	GTEx
rs9371504	RP11-350J20.9	cis	lung	GTEx
rs9371504	RP11-350J20.5	cis	Thyroid	GTEx
rs9371504	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs9371504	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs9371504	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs9371504	RP11-350J20.5	cis	Esophagus Mucosa	GTEx
rs9371504	NUP43	cis	Whole Blood	GTEx
rs9371504	RP11-350J20.5	cis	Artery Tibial	GTEx
rs9371504	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs9371504	RP11-350J20.5	cis	lung	GTEx
rs9371504	RAET1G	cis	Artery Tibial	GTEx
rs9371504	RP11-350J20.9	cis	Heart Left Ventricle	GTEx
rs9371504	C6orf72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150173000-150184200	Weak transcription	Aorta	Aorta
2	chr6:150180600-150184200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:150182000-150186200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr6:150182200-150184200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:150182200-150184200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:150182400-150184200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:150183200-150184200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr6:150183400-150184200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr6:150183400-150184400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr6:150183400-150184400	Flanking Active TSS	HUVEC	blood vessel
11	chr6:150183600-150184200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr6:150183600-150184200	Bivalent Enhancer	Fetal Thymus	thymus
13	chr6:150183600-150184200	Weak transcription	Gastric	stomach
14	chr6:150183600-150184400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:150183600-150184400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:150183600-150184400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:150183600-150185400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:150183600-150185600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:150183600-150185800	Active TSS	HSMMtube	muscle
20	chr6:150183600-150186000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:150183600-150186000	Active TSS	Duodenum Mucosa	Duodenum
22	chr6:150183600-150186000	Active TSS	Rectal Smooth Muscle	rectum
23	chr6:150183600-150186200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:150183600-150186200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:150183600-150186200	Active TSS	Brain Anterior Caudate	brain
26	chr6:150183600-150186200	Active TSS	NHLF	lung
27	chr6:150183600-150186400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:150183600-150186400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:150183600-150186400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:150183600-150186400	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr6:150183600-150186400	Active TSS	A549	lung
32	chr6:150183600-150186600	Active TSS	Brain Angular Gyrus	brain
33	chr6:150183800-150184200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
34	chr6:150183800-150184200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:150183800-150184200	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr6:150183800-150184200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:150183800-150184200	Flanking Active TSS	Fetal Stomach	stomach
38	chr6:150183800-150184400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr6:150183800-150184400	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr6:150183800-150184400	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr6:150183800-150184400	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr6:150183800-150184400	Flanking Active TSS	Placenta	Placenta
43	chr6:150183800-150184600	Flanking Active TSS	Fetal Muscle Trunk	muscle
44	chr6:150183800-150185200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:150183800-150185600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:150183800-150185600	Active TSS	Pancreas	Pancrea
47	chr6:150183800-150185600	Active TSS	Stomach Smooth Muscle	stomach
48	chr6:150183800-150185600	Active TSS	HMEC	breast
49	chr6:150183800-150185600	Active TSS	NHEK	skin
50	chr6:150183800-150185800	Active TSS	HepG2	liver

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