Variant report

Variant	rs1298878
Chromosome Location	chr4:8207154-8207155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr4:8207132-8207403	HUVEC	blood vessel:	n/a	chr4:8207277-8207288
2	SPI1	chr4:8207049-8207457	HL-60	blood:	n/a	n/a
3	POLR2A	chr4:8207148-8207236	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr4:8207077-8208103	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr4:8207040-8207447	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr4:8207110-8207425	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:8207119-8207169	NHBE	bronchial:	n/a
2	chr4:8207119-8207169	HRPEpiC	eye:	n/a
3	chr4:8207119-8207169	MCF-7	breast:	n/a
4	chr4:8207119-8207169	HNPCEpiC	eye:	n/a
5	chr4:8207119-8207169	HAEpiC	amniotic membrane:	n/a
6	chr4:8207119-8207169	NH-A	brain:	n/a
7	chr4:8207119-8207169	GM12892	blood:	n/a
8	chr4:8207119-8207169	BE2_C	brain:	n/a
9	chr4:8207119-8207169	NB4	blood:	n/a
10	chr4:8207119-8207169	GM12878	blood:	n/a
11	chr4:8207119-8207169	HIPEpiC	eye:	n/a
12	chr4:8207119-8207169	SKMC	muscle:	n/a
13	chr4:8207119-8207169	IMR90	lung:	fetal
14	chr4:8207119-8207169	CMK	blood:	n/a
15	chr4:8207119-8207169	HRCEpiC	kidney:	n/a
16	chr4:8207119-8207169	AG04450	lung:	fetal
17	chr4:8207119-8207169	RPTEC	kidney:	n/a
18	chr4:8207119-8207169	NT2-D1	testis:	n/a
19	chr4:8207119-8207169	SAEC	small airway:	n/a
20	chr4:8207119-8207169	K562	blood:	n/a
21	chr4:8207119-8207169	AG09309	skin:	n/a
22	chr4:8207119-8207169	HCM	heart:	n/a
23	chr4:8207119-8207169	Hela-S3	cervix:	n/a
24	chr4:8207119-8207169	H1-hESC	embryonic stem cell:	embryo
25	chr4:8207119-8207169	MCF10A-Er-Src	breast:	n/a
26	chr4:8207119-8207169	Caco-2	colon:	n/a
27	chr4:8207119-8207169	HMEC	breast:	n/a
28	chr4:8207119-8207169	PrEC	prostate:	n/a
29	chr4:8207119-8207169	NHDF-neo	bronchial:	n/a
30	chr4:8207119-8207169	GM19239	blood:	n/a
31	chr4:8207119-8207169	HepG2	liver:	n/a
32	chr4:8207119-8207169	HEEpiC	esophagus:	n/a
33	chr4:8207119-8207169	AG09319	gingival:	n/a
34	chr4:8207119-8207169	ECC-1	luminal epithelium:	n/a
35	chr4:8207119-8207169	HEK293	kidney:	embryo
36	chr4:8207119-8207169	ProgFib	skin:	n/a
37	chr4:8207119-8207169	T-47D	breast:	n/a
38	chr4:8207119-8207169	HCF	heart:	n/a
39	chr4:8207119-8207169	ovcar-3	ovarian:	n/a
40	chr4:8207119-8207169	HRE	kidney:	n/a
41	chr4:8207119-8207169	GM06990	blood:	n/a
42	chr4:8207119-8207169	HPAEpiC	pulmonary alveolar:	n/a
43	chr4:8207119-8207169	U87	brain:	n/a
44	chr4:8207119-8207169	AoSMC	blood vessel:	n/a
45	chr4:8207119-8207169	Hepatocyte	liver:	n/a
46	chr4:8207119-8207169	A549	lung:	n/a
47	chr4:8207119-8207169	HL-60	blood:	n/a
48	chr4:8207119-8207169	HCPEpiC	choroid plexus:	n/a
49	chr4:8207119-8207169	HCT-116	colon:	n/a
50	chr4:8207119-8207169	AG04449	skin:	fetal

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:8201150..8205648-chr4:8206751..8210488,5	MCF-7	breast:
2	chr4:8206620..8209251-chr4:8213740..8215490,2	MCF-7	breast:
3	chr4:8204604..8207320-chr4:8213479..8215268,2	K562	blood:
4	chr4:8205263..8208734-chr4:8209545..8212035,3	MCF-7	breast:
5	chr4:8202798..8206403-chr4:8207013..8209683,3	K562	blood:
6	chr4:8196365..8198460-chr4:8203921..8207190,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HTRA3-5	chr4:8206894-8207339	NONHSAT095078

No data

Variant related genes	Relation type
SH3TC1	TF binding region
SH3TC1	CpG island
ENSG00000125089	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1281130	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281131	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678263	0.86[EUR][1000 genomes]
rs1678269	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2677605	0.95[ASN][1000 genomes]
rs922521	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010809	chr4:8097627-8292324	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv878593	chr4:8125788-8233341	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv461216	chr4:8154534-8276411	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv593626	chr4:8154534-8276411	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv878594	chr4:8154534-8286916	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv878595	chr4:8154534-8390646	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv470012	chr4:8171401-8233341	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv878596	chr4:8171401-8254784	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv878597	chr4:8171401-8294196	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv829853	chr4:8172065-8320868	Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv869928	chr4:8195069-8214848	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv878598	chr4:8195705-8254784	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv878599	chr4:8195705-8293398	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	esv2763338	chr4:8199091-8260812	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv1831794	chr4:8199833-8233341	Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv593627	chr4:8202211-8311043	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
18	esv3405589	chr4:8204602-8207400	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8202600-8207600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:8203000-8216200	Weak transcription	Osteobl	bone
3	chr4:8203000-8216400	Weak transcription	Hela-S3	cervix
4	chr4:8203200-8208800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:8203200-8222400	Weak transcription	Brain Substantia Nigra	brain
6	chr4:8203400-8207600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:8203400-8210800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:8203400-8216400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:8203400-8216600	Weak transcription	Right Atrium	heart
10	chr4:8203600-8207600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:8203600-8208400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:8203600-8208400	Genic enhancers	Spleen	Spleen
13	chr4:8203600-8211200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:8203600-8216600	Weak transcription	Left Ventricle	heart
15	chr4:8203800-8216600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:8203800-8216600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr4:8203800-8224800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:8204000-8207400	Genic enhancers	HMEC	breast
19	chr4:8204000-8208400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr4:8204000-8209200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:8204000-8216600	Weak transcription	Brain Anterior Caudate	brain
22	chr4:8204200-8212200	Weak transcription	Fetal Kidney	kidney
23	chr4:8204200-8216000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr4:8204400-8208000	Genic enhancers	HUVEC	blood vessel
25	chr4:8204600-8207800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:8204600-8208000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr4:8204600-8218800	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:8204800-8207600	Enhancers	Primary B cells from cord blood	blood
29	chr4:8204800-8208400	Genic enhancers	Placenta	Placenta
30	chr4:8204800-8209200	Weak transcription	Primary T cells from cord blood	blood
31	chr4:8204800-8222600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr4:8205000-8207400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:8205000-8207600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:8205000-8210400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr4:8205000-8211400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:8205000-8219200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr4:8205200-8207600	Weak transcription	Colonic Mucosa	Colon
38	chr4:8205200-8208000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr4:8205200-8209000	Enhancers	Dnd41	blood
40	chr4:8205200-8212400	Genic enhancers	Primary monocytes fromperipheralblood	blood
41	chr4:8205200-8219800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:8205400-8207200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr4:8205400-8207600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr4:8205400-8207600	Strong transcription	Pancreas	Pancrea
45	chr4:8205400-8207600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr4:8205400-8208200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:8205400-8208200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:8205400-8209000	Enhancers	Primary hematopoietic stem cells	blood
49	chr4:8205600-8207600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr4:8205600-8208200	Enhancers	Placenta Amnion	Placenta Amnion

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