Variant report

Variant	rs11678616
Chromosome Location	chr2:209004548-209004549
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	chr2:209004513-209004563	SK-N-SH	brain:	n/a
2	chr2:209004513-209004563	BJ	skin:	n/a
3	chr2:209004513-209004563	HPAEpiC	pulmonary alveolar:	n/a
4	chr2:209004513-209004563	HepG2	liver:	n/a
5	chr2:209004513-209004563	PFSK-1	brain:	n/a
6	chr2:209004513-209004563	BE2_C	brain:	n/a
7	chr2:209004513-209004563	CMK	blood:	n/a
8	chr2:209004513-209004563	Caco-2	colon:	n/a
9	chr2:209004513-209004563	PANC-1	pancreas:	n/a
10	chr2:209004513-209004563	SK-N-MC	brain:	n/a
11	chr2:209004513-209004563	GM19239	blood:	n/a
12	chr2:209004513-209004563	NHBE	bronchial:	n/a
13	chr2:209004513-209004563	GM12892	blood:	n/a
14	chr2:209004513-209004563	Hepatocyte	liver:	n/a
15	chr2:209004513-209004563	AG04450	lung:	fetal
16	chr2:209004513-209004563	HL-60	blood:	n/a
17	chr2:209004513-209004563	HEK293	kidney:	embryo
18	chr2:209004513-209004563	AG09319	gingival:	n/a
19	chr2:209004513-209004563	GM12891	blood:	n/a
20	chr2:209004513-209004563	IMR90	lung:	fetal
21	chr2:209004513-209004563	MCF10A-Er-Src	breast:	n/a
22	chr2:209004513-209004563	HAEpiC	amniotic membrane:	n/a
23	chr2:209004513-209004563	NHDF-neo	bronchial:	n/a
24	chr2:209004513-209004563	HMEC	breast:	n/a
25	chr2:209004513-209004563	T-47D	breast:	n/a
26	chr2:209004513-209004563	HNPCEpiC	eye:	n/a
27	chr2:209004513-209004563	MCF-7	breast:	n/a
28	chr2:209004513-209004563	SKMC	muscle:	n/a
29	chr2:209004513-209004563	AG09309	skin:	n/a
30	chr2:209004513-209004563	SAEC	small airway:	n/a
31	chr2:209004513-209004563	HUVEC	blood vessel:	n/a
32	chr2:209004513-209004563	U87	brain:	n/a
33	chr2:209004513-209004563	AoSMC	blood vessel:	n/a
34	chr2:209004513-209004563	HCF	heart:	n/a
35	chr2:209004513-209004563	K562	blood:	n/a
36	chr2:209004513-209004563	Jurkat	blood:	n/a
37	chr2:209004513-209004563	HCT-116	colon:	n/a
38	chr2:209004513-209004563	HRCEpiC	kidney:	n/a
39	chr2:209004513-209004563	NB4	blood:	n/a
40	chr2:209004513-209004563	GM12878	blood:	n/a
41	chr2:209004513-209004563	ProgFib	skin:	n/a
42	chr2:209004513-209004563	ovcar-3	ovarian:	n/a
43	chr2:209004513-209004563	HEEpiC	esophagus:	n/a
44	chr2:209004513-209004563	RPTEC	kidney:	n/a
45	chr2:209004513-209004563	A549	lung:	n/a
46	chr2:209004513-209004563	H1-hESC	embryonic stem cell:	embryo
47	chr2:209004513-209004563	PrEC	prostate:	n/a
48	chr2:209004513-209004563	HCM	heart:	n/a
49	chr2:209004513-209004563	ECC-1	luminal epithelium:	n/a
50	chr2:209004513-209004563	HCPEpiC	choroid plexus:	n/a

No data

Variant related genes	Relation type
ENSG00000224529	CpG island

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11679743	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12464752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13007922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242071	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4263096	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4276012	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4289171	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4338947	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4375849	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4449112	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4583446	0.90[JPT][hapmap]
rs6435416	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6710715	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6711499	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6751246	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs796282	0.81[ASN][1000 genomes]
rs796287	0.82[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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer 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
4	nsv875747	chr2:208990345-209042963	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv875748	chr2:208994399-209033557	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209001800-209006800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr2:209004000-209004600	Enhancers	HMEC	breast
3	chr2:209004400-209006800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:209004400-209012800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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