Variant report

Variant	rs28527279
Chromosome Location	chr2:86948835-86948836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:86946162-86949537	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr2:86948792-86949146	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:86948821-86949036	GM12878	blood:	n/a	n/a
4	MXI1	chr2:86946786-86948908	SK-N-SH	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:86948810-86948860	CMK	blood:	n/a
2	chr2:86948810-86948860	HCT-116	colon:	n/a
3	chr2:86948810-86948860	ovcar-3	ovarian:	n/a
4	chr2:86948810-86948860	PrEC	prostate:	n/a
5	chr2:86948810-86948860	HRPEpiC	eye:	n/a
6	chr2:86948810-86948860	SK-N-SH_RA	brain:	n/a
7	chr2:86948810-86948860	GM12892	blood:	n/a
8	chr2:86948810-86948860	HEK293	kidney:	embryo
9	chr2:86948810-86948860	HNPCEpiC	eye:	n/a
10	chr2:86948810-86948860	NHDF-neo	bronchial:	n/a
11	chr2:86948810-86948860	GM06990	blood:	n/a
12	chr2:86948810-86948860	HMEC	breast:	n/a
13	chr2:86948810-86948860	RPTEC	kidney:	n/a
14	chr2:86948810-86948860	HEEpiC	esophagus:	n/a
15	chr2:86948810-86948860	GM12891	blood:	n/a
16	chr2:86948810-86948860	GM19239	blood:	n/a
17	chr2:86948810-86948860	ProgFib	skin:	n/a
18	chr2:86948810-86948860	T-47D	breast:	n/a
19	chr2:86948810-86948860	SK-N-MC	brain:	n/a
20	chr2:86948810-86948860	GM12878	blood:	n/a
21	chr2:86948810-86948860	U87	brain:	n/a
22	chr2:86948810-86948860	HIPEpiC	eye:	n/a
23	chr2:86948810-86948860	HPAEpiC	pulmonary alveolar:	n/a
24	chr2:86948810-86948860	HL-60	blood:	n/a
25	chr2:86948810-86948860	A549	lung:	n/a
26	chr2:86948810-86948860	PANC-1	pancreas:	n/a
27	chr2:86948810-86948860	AG09319	gingival:	n/a
28	chr2:86948810-86948860	BE2_C	brain:	n/a
29	chr2:86948810-86948860	HRE	kidney:	n/a
30	chr2:86948810-86948860	BJ	skin:	n/a
31	chr2:86948810-86948860	MCF-7	breast:	n/a
32	chr2:86948810-86948860	Jurkat	blood:	n/a
33	chr2:86948810-86948860	Hela-S3	cervix:	n/a
34	chr2:86948810-86948860	LNCaP	prostate:	n/a
35	chr2:86948810-86948860	NB4	blood:	n/a
36	chr2:86948810-86948860	AG09309	skin:	n/a
37	chr2:86948810-86948860	IMR90	lung:	fetal
38	chr2:86948810-86948860	AoSMC	blood vessel:	n/a
39	chr2:86948810-86948860	Hepatocyte	liver:	n/a
40	chr2:86948810-86948860	AG04450	lung:	fetal
41	chr2:86948810-86948860	HAEpiC	amniotic membrane:	n/a
42	chr2:86948810-86948860	HCM	heart:	n/a
43	chr2:86948810-86948860	ECC-1	luminal epithelium:	n/a
44	chr2:86948810-86948860	AG04449	skin:	fetal
45	chr2:86948810-86948860	NHBE	bronchial:	n/a
46	chr2:86948810-86948860	AG10803	skin:	n/a
47	chr2:86948810-86948860	NH-A	brain:	n/a
48	chr2:86948810-86948860	SKMC	muscle:	n/a
49	chr2:86948810-86948860	Caco-2	colon:	n/a
50	chr2:86948810-86948860	HCPEpiC	choroid plexus:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86849761..86852664-chr2:86946875..86949825,4	MCF-7	breast:
2	chr2:86848500..86851973-chr2:86945425..86949651,4	MCF-7	breast:

No data

Variant related genes	Relation type
CHMP3	TF binding region
RNF103-CHMP3	TF binding region
CHMP3	CpG island
RNF103-CHMP3	CpG island
ENSG00000249884	Chromatin interaction
ENSG00000239305	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10209550	1.00[ASN][1000 genomes]
rs12714202	0.93[CEU][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs13010845	1.00[ASN][1000 genomes]
rs1400032	1.00[ASN][1000 genomes]
rs2271666	0.94[CEU][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs308917	1.00[ASN][1000 genomes]
rs308918	1.00[ASN][1000 genomes]
rs4832307	1.00[ASN][1000 genomes]
rs6547705	0.89[ASN][1000 genomes]
rs6750263	1.00[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	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv961802	chr2:86933414-86958321	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv10063	chr2:86940988-87084360	Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1002420	chr2:86948835-87172715	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86946200-86949000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:86946200-86949000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:86946200-86949000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr2:86946200-86949000	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr2:86946200-86949000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr2:86946200-86949000	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr2:86946200-86949000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:86946200-86949000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:86946200-86949000	Active TSS	Muscle Satellite Cultured Cells	--
10	chr2:86946200-86949000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:86946200-86949000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:86946200-86949000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:86946200-86949000	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr2:86946200-86949000	Active TSS	Rectal Smooth Muscle	rectum
15	chr2:86946600-86949000	Active TSS	H1 Cell Line	embryonic stem cell
16	chr2:86946600-86949000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:86946600-86949000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:86946600-86949000	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr2:86946600-86949000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:86946600-86949000	Active TSS	Fetal Brain Female	brain
21	chr2:86946600-86949000	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr2:86946600-86949000	Active TSS	Stomach Smooth Muscle	stomach
23	chr2:86946600-86949000	Active TSS	HSMM	muscle
24	chr2:86946800-86949000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:86946800-86949000	Active TSS	H9 Cell Line	embryonic stem cell
26	chr2:86946800-86949000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:86946800-86949000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:86946800-86949000	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr2:86946800-86949000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:86946800-86949000	Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr2:86946800-86949000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:86946800-86949000	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr2:86946800-86949000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:86946800-86949000	Active TSS	Liver	Liver
35	chr2:86946800-86949000	Active TSS	Brain Angular Gyrus	brain
36	chr2:86946800-86949000	Active TSS	Brain Cingulate Gyrus	brain
37	chr2:86946800-86949000	Active TSS	Brain Hippocampus Middle	brain
38	chr2:86946800-86949000	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr2:86946800-86949000	Active TSS	Colonic Mucosa	Colon
40	chr2:86946800-86949000	Active TSS	Colon Smooth Muscle	Colon
41	chr2:86946800-86949000	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr2:86946800-86949000	Active TSS	Esophagus	oesophagus
43	chr2:86946800-86949000	Active TSS	Fetal Intestine Large	intestine
44	chr2:86946800-86949000	Active TSS	Fetal Intestine Small	intestine
45	chr2:86946800-86949000	Active TSS	Left Ventricle	heart
46	chr2:86946800-86949000	Active TSS	Ovary	ovary
47	chr2:86946800-86949000	Active TSS	Psoas Muscle	Psoas
48	chr2:86946800-86949000	Active TSS	Right Atrium	heart
49	chr2:86946800-86949000	Active TSS	Right Ventricle	heart
50	chr2:86946800-86949000	Active TSS	Thymus	Thymus

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