Variant report

Variant	rs2534873
Chromosome Location	chr7:84816889-84816890
allele	A/G
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	KAP1	chr7:84814820-84817472	HEK293	kidney:	n/a	chr7:84815837-84815845
2	SMC3	chr7:84813820-84817583	SK-N-SH	brain:	n/a	chr7:84815619-84815627 chr7:84816197-84816207 chr7:84815764-84815774
3	SIN3A	chr7:84814259-84816923	H1-hESC	embryonic stem cell:	n/a	chr7:84816341-84816349 chr7:84816342-84816355
4	CTCF	chr7:84814337-84817030	SK-N-SH	brain:	n/a	chr7:84814916-84814929 chr7:84815761-84815774 chr7:84814922-84814935 chr7:84815992-84816000 chr7:84816175-84816188 chr7:84816252-84816265 chr7:84814919-84814932
5	MAZ	chr7:84815578-84816931	IMR90	lung:	n/a	chr7:84816194-84816204
6	ZNF263	chr7:84814225-84816901	HEK293-T-REx	kidney:	n/a	chr7:84816270-84816291 chr7:84816269-84816278 chr7:84816419-84816428

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:84816843-84816893	HMEC	breast:	n/a
2	chr7:84816843-84816893	AG09319	gingival:	n/a
3	chr7:84816843-84816893	PrEC	prostate:	n/a
4	chr7:84816843-84816893	IMR90	lung:	fetal
5	chr7:84816843-84816893	HRCEpiC	kidney:	n/a
6	chr7:84816843-84816893	SK-N-SH_RA	brain:	n/a
7	chr7:84816843-84816893	Caco-2	colon:	n/a
8	chr7:84816843-84816893	GM19239	blood:	n/a
9	chr7:84816843-84816893	HRPEpiC	eye:	n/a
10	chr7:84816843-84816893	SKMC	muscle:	n/a
11	chr7:84816843-84816893	Hela-S3	cervix:	n/a
12	chr7:84816843-84816893	ECC-1	luminal epithelium:	n/a
13	chr7:84816843-84816893	HAEpiC	amniotic membrane:	n/a
14	chr7:84816843-84816893	AG04449	skin:	fetal
15	chr7:84816843-84816893	HNPCEpiC	eye:	n/a
16	chr7:84816843-84816893	K562	blood:	n/a
17	chr7:84816843-84816893	SK-N-SH	brain:	n/a
18	chr7:84816843-84816893	NT2-D1	testis:	n/a
19	chr7:84816843-84816893	Jurkat	blood:	n/a
20	chr7:84816843-84816893	HepG2	liver:	n/a
21	chr7:84816843-84816893	GM12892	blood:	n/a
22	chr7:84816843-84816893	Hepatocyte	liver:	n/a
23	chr7:84816843-84816893	HCF	heart:	n/a
24	chr7:84816843-84816893	HPAEpiC	pulmonary alveolar:	n/a
25	chr7:84816843-84816893	H1-hESC	embryonic stem cell:	embryo
26	chr7:84816843-84816893	HIPEpiC	eye:	n/a
27	chr7:84816843-84816893	HEK293	kidney:	embryo
28	chr7:84816843-84816893	GM06990	blood:	n/a
29	chr7:84816843-84816893	CMK	blood:	n/a
30	chr7:84816843-84816893	BJ	skin:	n/a
31	chr7:84816843-84816893	NH-A	brain:	n/a
32	chr7:84816843-84816893	PFSK-1	brain:	n/a
33	chr7:84816843-84816893	BE2_C	brain:	n/a
34	chr7:84816843-84816893	NB4	blood:	n/a
35	chr7:84816843-84816893	NHDF-neo	bronchial:	n/a
36	chr7:84816843-84816893	AG04450	lung:	fetal
37	chr7:84816843-84816893	SAEC	small airway:	n/a
38	chr7:84816843-84816893	HRE	kidney:	n/a
39	chr7:84816843-84816893	AoSMC	blood vessel:	n/a
40	chr7:84816843-84816893	AG10803	skin:	n/a
41	chr7:84816843-84816893	MCF-7	breast:	n/a
42	chr7:84816843-84816893	LNCaP	prostate:	n/a
43	chr7:84816843-84816893	A549	lung:	n/a
44	chr7:84816843-84816893	HCM	heart:	n/a
45	chr7:84816843-84816893	PANC-1	pancreas:	n/a
46	chr7:84816843-84816893	NHBE	bronchial:	n/a
47	chr7:84816843-84816893	U87	brain:	n/a
48	chr7:84816843-84816893	HUVEC	blood vessel:	n/a
49	chr7:84816843-84816893	HCT-116	colon:	n/a
50	chr7:84816843-84816893	AG09309	skin:	n/a

Variant related genes	Relation type
SEMA3D	TF binding region
SEMA3D	CpG island

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs17562848	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17648312	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215436	0.92[ASN][1000 genomes]
rs2240890	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2534854	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2534866	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2534867	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2534872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732749	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2732751	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732754	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2732755	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2732757	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2732762	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34319950	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56918106	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61131189	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62462192	0.80[ASN][1000 genomes]
rs62462197	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62462217	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422324	chr7:84530290-84944913	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv916645	chr7:84678606-85420011	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv869255	chr7:84678606-85444155	Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv888645	chr7:84738495-84842884	Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv888646	chr7:84754151-84905855	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:84814400-84817000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:84814400-84817000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr7:84814400-84817000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:84814600-84817000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr7:84814600-84817000	Active TSS	Fetal Kidney	kidney
6	chr7:84814800-84817000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:84815200-84817000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
8	chr7:84816400-84817000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:84816400-84817000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
10	chr7:84816400-84817000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
11	chr7:84816400-84817200	Flanking Active TSS	Fetal Lung	lung
12	chr7:84816600-84817000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:84816600-84817000	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
14	chr7:84816600-84817000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:84816600-84817000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
16	chr7:84816600-84817000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:84816600-84817000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:84816600-84817000	Enhancers	Primary B cells from peripheral blood	blood
19	chr7:84816600-84817000	Enhancers	Fetal Heart	heart
20	chr7:84816600-84817200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:84816600-84817400	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr7:84816800-84817000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
23	chr7:84816800-84817000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:84816800-84817000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr7:84816800-84817000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr7:84816800-84817000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:84816800-84817000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr7:84816800-84817000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr7:84816800-84817000	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
30	chr7:84816800-84817000	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr7:84816800-84817000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr7:84816800-84817000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:84816800-84817000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:84816800-84817000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr7:84816800-84817000	Bivalent/Poised TSS	Adipose Nuclei	Adipose
36	chr7:84816800-84817000	Enhancers	Brain Anterior Caudate	brain
37	chr7:84816800-84817000	Bivalent Enhancer	Brain Germinal Matrix	brain
38	chr7:84816800-84817000	Enhancers	Brain Hippocampus Middle	brain
39	chr7:84816800-84817000	Enhancers	Brain Substantia Nigra	brain
40	chr7:84816800-84817000	Enhancers	Colonic Mucosa	Colon
41	chr7:84816800-84817000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
42	chr7:84816800-84817000	Bivalent Enhancer	Fetal Brain Female	brain
43	chr7:84816800-84817000	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr7:84816800-84817000	Active TSS	Fetal Stomach	stomach
45	chr7:84816800-84817000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
46	chr7:84816800-84817000	Enhancers	HMEC	breast
47	chr7:84816800-84817000	Enhancers	HUVEC	blood vessel
48	chr7:84816800-84817000	Bivalent/Poised TSS	NH-A	brain
49	chr7:84816800-84817000	Active TSS	NHDF-Ad	bronchial
50	chr7:84816800-84817000	Enhancers	NHEK	skin

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