Variant report

Variant	rs12994872
Chromosome Location	chr2:48983222-48983223
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:48983189-48983239	HRPEpiC	eye:	n/a
2	chr2:48983178-48983228	LNCaP	prostate:	n/a
3	chr2:48983189-48983239	AG10803	skin:	n/a
4	chr2:48983189-48983239	U87	brain:	n/a
5	chr2:48983189-48983239	HCF	heart:	n/a
6	chr2:48983189-48983239	PFSK-1	brain:	n/a
7	chr2:48983178-48983228	HepG2	liver:	n/a
8	chr2:48983178-48983228	NH-A	brain:	n/a
9	chr2:48983178-48983228	NHDF-neo	bronchial:	n/a
10	chr2:48983189-48983239	GM12878	blood:	n/a
11	chr2:48983178-48983228	CMK	blood:	n/a
12	chr2:48983178-48983228	HCPEpiC	choroid plexus:	n/a
13	chr2:48983178-48983228	HUVEC	blood vessel:	n/a
14	chr2:48983189-48983239	AG04449	skin:	fetal
15	chr2:48983178-48983228	HAEpiC	amniotic membrane:	n/a
16	chr2:48983178-48983228	AG04450	lung:	fetal
17	chr2:48983189-48983239	ECC-1	luminal epithelium:	n/a
18	chr2:48983178-48983228	SK-N-SH_RA	brain:	n/a
19	chr2:48983178-48983228	PANC-1	pancreas:	n/a
20	chr2:48983178-48983228	NB4	blood:	n/a
21	chr2:48983189-48983239	SAEC	small airway:	n/a
22	chr2:48983189-48983239	H1-hESC	embryonic stem cell:	embryo
23	chr2:48983178-48983228	HRPEpiC	eye:	n/a
24	chr2:48983178-48983228	AG09309	skin:	n/a
25	chr2:48983189-48983239	ovcar-3	ovarian:	n/a
26	chr2:48983178-48983228	BJ	skin:	n/a
27	chr2:48983178-48983228	HL-60	blood:	n/a
28	chr2:48983189-48983239	IMR90	lung:	fetal
29	chr2:48983178-48983228	U87	brain:	n/a
30	chr2:48983189-48983239	GM19239	blood:	n/a
31	chr2:48983189-48983239	HepG2	liver:	n/a
32	chr2:48983178-48983228	MCF10A-Er-Src	breast:	n/a
33	chr2:48983189-48983239	HMEC	breast:	n/a
34	chr2:48983189-48983239	HCM	heart:	n/a
35	chr2:48983189-48983239	K562	blood:	n/a
36	chr2:48983178-48983228	BE2_C	brain:	n/a
37	chr2:48983189-48983239	A549	lung:	n/a
38	chr2:48983178-48983228	GM12878	blood:	n/a
39	chr2:48983189-48983239	GM12891	blood:	n/a
40	chr2:48983189-48983239	GM06990	blood:	n/a
41	chr2:48983178-48983228	SK-N-SH	brain:	n/a
42	chr2:48983178-48983228	GM19239	blood:	n/a
43	chr2:48983189-48983239	SK-N-SH_RA	brain:	n/a
44	chr2:48983189-48983239	Jurkat	blood:	n/a
45	chr2:48983189-48983239	HCT-116	colon:	n/a
46	chr2:48983178-48983228	NHBE	bronchial:	n/a
47	chr2:48983189-48983239	CMK	blood:	n/a
48	chr2:48983178-48983228	HCT-116	colon:	n/a
49	chr2:48983189-48983239	SK-N-MC	brain:	n/a
50	chr2:48983178-48983228	AG04449	skin:	fetal

No data

Variant related genes	Relation type
LHCGR	CpG island

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13007390	1.00[AFR][1000 genomes]
rs13015021	1.00[AFR][1000 genomes]
rs13029423	0.92[ASN][1000 genomes]
rs35429744	0.89[ASN][1000 genomes]
rs71407516	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv833992	chr2:48814223-48998037	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48982800-48983800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:48983200-48983400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
3	chr2:48983200-48983400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
4	chr2:48983200-48983400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
5	chr2:48983200-48983400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell

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