Variant report

Variant	rs4931176
Chromosome Location	chr12:29538269-29538270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:29538243-29538293	MCF-7	breast:	n/a
2	chr12:29538243-29538293	IMR90	lung:	fetal
3	chr12:29538243-29538293	BJ	skin:	n/a
4	chr12:29538243-29538293	ECC-1	luminal epithelium:	n/a
5	chr12:29538243-29538293	GM12878	blood:	n/a
6	chr12:29538243-29538293	HEK293	kidney:	embryo
7	chr12:29538243-29538293	AG09309	skin:	n/a
8	chr12:29538243-29538293	HCT-116	colon:	n/a
9	chr12:29538243-29538293	Jurkat	blood:	n/a
10	chr12:29538243-29538293	SKMC	muscle:	n/a
11	chr12:29538243-29538293	Hepatocyte	liver:	n/a
12	chr12:29538243-29538293	PrEC	prostate:	n/a
13	chr12:29538243-29538293	NHDF-neo	bronchial:	n/a
14	chr12:29538243-29538293	NH-A	brain:	n/a
15	chr12:29538243-29538293	GM06990	blood:	n/a
16	chr12:29538243-29538293	NT2-D1	testis:	n/a
17	chr12:29538243-29538293	NHBE	bronchial:	n/a
18	chr12:29538243-29538293	K562	blood:	n/a
19	chr12:29538243-29538293	T-47D	breast:	n/a
20	chr12:29538243-29538293	BE2_C	brain:	n/a
21	chr12:29538243-29538293	PANC-1	pancreas:	n/a
22	chr12:29538243-29538293	ProgFib	skin:	n/a
23	chr12:29538243-29538293	HepG2	liver:	n/a
24	chr12:29538243-29538293	SK-N-SH_RA	brain:	n/a
25	chr12:29538243-29538293	HCM	heart:	n/a
26	chr12:29538243-29538293	HIPEpiC	eye:	n/a
27	chr12:29538243-29538293	GM19239	blood:	n/a
28	chr12:29538243-29538293	AoSMC	blood vessel:	n/a
29	chr12:29538243-29538293	MCF10A-Er-Src	breast:	n/a
30	chr12:29538243-29538293	RPTEC	kidney:	n/a
31	chr12:29538243-29538293	CMK	blood:	n/a
32	chr12:29538243-29538293	Hela-S3	cervix:	n/a
33	chr12:29538243-29538293	HCPEpiC	choroid plexus:	n/a
34	chr12:29538243-29538293	LNCaP	prostate:	n/a
35	chr12:29538243-29538293	AG04449	skin:	fetal
36	chr12:29538243-29538293	AG09319	gingival:	n/a
37	chr12:29538243-29538293	AG04450	lung:	fetal
38	chr12:29538243-29538293	SK-N-SH	brain:	n/a
39	chr12:29538243-29538293	A549	lung:	n/a
40	chr12:29538243-29538293	HMEC	breast:	n/a
41	chr12:29538243-29538293	HRPEpiC	eye:	n/a
42	chr12:29538243-29538293	NB4	blood:	n/a
43	chr12:29538243-29538293	HCF	heart:	n/a
44	chr12:29538243-29538293	HRE	kidney:	n/a
45	chr12:29538243-29538293	PFSK-1	brain:	n/a
46	chr12:29538243-29538293	U87	brain:	n/a
47	chr12:29538243-29538293	HEEpiC	esophagus:	n/a
48	chr12:29538243-29538293	HL-60	blood:	n/a
49	chr12:29538243-29538293	HPAEpiC	pulmonary alveolar:	n/a
50	chr12:29538243-29538293	HRCEpiC	kidney:	n/a

No data

Variant related genes	Relation type
ERGIC2	CpG island
OVCH1-AS1	CpG island

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10082724	0.85[CEU][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes]
rs10161279	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843388	0.85[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs10843393	0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11050164	0.94[YRI][hapmap]
rs11050165	0.94[YRI][hapmap]
rs11050210	0.97[EUR][1000 genomes]
rs11050211	0.93[YRI][hapmap]
rs12297776	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304413	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311187	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316548	0.94[YRI][hapmap]
rs12319953	0.81[AFR][1000 genomes]
rs16934110	0.86[ASW][hapmap];0.91[LWK][hapmap];0.94[YRI][hapmap]
rs16934124	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16934148	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16934161	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3782514	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6487798	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7306412	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7309132	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs7312068	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4931176	RP11-996F15.2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29535600-29542600	Weak transcription	Hela-S3	cervix
2	chr12:29535600-29543400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:29537800-29538400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr12:29537800-29538400	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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