Variant report

Variant	rs61949616
Chromosome Location	chr12:87232859-87232860
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr12:87232056-87233179	H1-neurons	neurons:	n/a	n/a
2	RAD21	chr12:87232622-87232944	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr12:87232720-87232870	HPAF	blood vessel:	n/a	n/a
4	CTCF	chr12:87232750-87232860	LNCaP	prostate:	n/a	n/a
5	CTCF	chr12:87232720-87232870	HCPEpiC	choroid plexus:	n/a	n/a
6	RAD21	chr12:87232607-87232865	SK-N-SH_RA	brain:	n/a	n/a
7	CTCF	chr12:87232760-87232910	BE2_C	brain:	n/a	n/a
8	RAD21	chr12:87232676-87232868	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr12:87232840-87232990	BE2_C	brain:	n/a	n/a
10	POLR2A	chr12:87232433-87232943	H1-neurons	neurons:	n/a	n/a
11	CTCF	chr12:87232740-87232890	HPF	lung:	n/a	n/a
12	CTCF	chr12:87232740-87232890	HPAF	blood vessel:	n/a	n/a
13	RAD21	chr12:87232675-87232902	SK-N-SH_RA	brain:	n/a	n/a
14	REST	chr12:87232342-87233045	H1-neurons	neurons:	n/a	n/a
15	CTCF	chr12:87232723-87232862	Medullo	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:87232821-87232871	AG09319	gingival:	n/a
2	chr12:87232821-87232871	K562	blood:	n/a
3	chr12:87232821-87232871	NH-A	brain:	n/a
4	chr12:87232821-87232871	NT2-D1	testis:	n/a
5	chr12:87232821-87232871	AoSMC	blood vessel:	n/a
6	chr12:87232821-87232871	HEEpiC	esophagus:	n/a
7	chr12:87232821-87232871	H1-hESC	embryonic stem cell:	embryo
8	chr12:87232821-87232871	HIPEpiC	eye:	n/a
9	chr12:87232821-87232871	HCPEpiC	choroid plexus:	n/a
10	chr12:87232821-87232871	T-47D	breast:	n/a
11	chr12:87232821-87232871	SAEC	small airway:	n/a
12	chr12:87232821-87232871	HCM	heart:	n/a
13	chr12:87232821-87232871	Caco-2	colon:	n/a
14	chr12:87232821-87232871	HCT-116	colon:	n/a
15	chr12:87232821-87232871	HPAEpiC	pulmonary alveolar:	n/a
16	chr12:87232821-87232871	MCF-7	breast:	n/a
17	chr12:87232821-87232871	ProgFib	skin:	n/a
18	chr12:87232821-87232871	AG09309	skin:	n/a
19	chr12:87232821-87232871	Hepatocyte	liver:	n/a
20	chr12:87232821-87232871	ECC-1	luminal epithelium:	n/a
21	chr12:87232821-87232871	HepG2	liver:	n/a
22	chr12:87232821-87232871	BE2_C	brain:	n/a
23	chr12:87232821-87232871	NHBE	bronchial:	n/a
24	chr12:87232821-87232871	GM12878	blood:	n/a
25	chr12:87232821-87232871	HRPEpiC	eye:	n/a
26	chr12:87232821-87232871	SK-N-MC	brain:	n/a
27	chr12:87232821-87232871	HMEC	breast:	n/a
28	chr12:87232821-87232871	SK-N-SH_RA	brain:	n/a
29	chr12:87232821-87232871	U87	brain:	n/a
30	chr12:87232821-87232871	LNCaP	prostate:	n/a
31	chr12:87232821-87232871	PrEC	prostate:	n/a
32	chr12:87232821-87232871	Hela-S3	cervix:	n/a
33	chr12:87232821-87232871	PANC-1	pancreas:	n/a
34	chr12:87232821-87232871	CMK	blood:	n/a
35	chr12:87232821-87232871	RPTEC	kidney:	n/a
36	chr12:87232821-87232871	IMR90	lung:	fetal
37	chr12:87232821-87232871	GM19239	blood:	n/a
38	chr12:87232821-87232871	GM06990	blood:	n/a
39	chr12:87232821-87232871	A549	lung:	n/a
40	chr12:87232821-87232871	PFSK-1	brain:	n/a
41	chr12:87232821-87232871	SKMC	muscle:	n/a
42	chr12:87232821-87232871	AG04449	skin:	fetal
43	chr12:87232821-87232871	SK-N-SH	brain:	n/a
44	chr12:87232821-87232871	NHDF-neo	bronchial:	n/a
45	chr12:87232821-87232871	GM12892	blood:	n/a
46	chr12:87232821-87232871	HCF	heart:	n/a
47	chr12:87232821-87232871	GM12891	blood:	n/a
48	chr12:87232821-87232871	Jurkat	blood:	n/a
49	chr12:87232821-87232871	HAEpiC	amniotic membrane:	n/a
50	chr12:87232821-87232871	HRE	kidney:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MGAT4C-1	chr12:87232443-87232905	ENSG00000258185

No data

Variant related genes	Relation type
MGAT4C	TF binding region
ENSG00000258185	TF binding region
ENSG00000258185	CpG island
MGAT4C	CpG island

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

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

rs_ID	r²[population]
rs11835356	0.81[AMR][1000 genomes]
rs55789636	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61949615	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61949617	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73183105	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754127	chr12:86723232-87576932	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv916862	chr12:86837694-87718558	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv899396	chr12:86863041-87276957	ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv899397	chr12:86863041-87636831	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv916604	chr12:86966256-87275268	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1049580	chr12:86966497-87354132	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv559692	chr12:87098055-87263693	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv455682	chr12:87194510-87274871	Active TSS Flanking Active TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv868879	chr12:87207243-87578373	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv559693	chr12:87216285-87447757	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1049688	chr12:87219949-87412043	Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1052693	chr12:87219949-87573582	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv559694	chr12:87224415-87274871	Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv899401	chr12:87225050-87287609	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv899402	chr12:87225050-87287609	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv899403	chr12:87225050-87528020	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv2753551	chr12:87226774-87473947	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:87229400-87233200	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr12:87231000-87233000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:87231200-87233000	Enhancers	H1 Cell Line	embryonic stem cell
4	chr12:87232200-87233000	Active TSS	Brain Angular Gyrus	brain
5	chr12:87232600-87233200	Weak transcription	Fetal Brain Male	brain
6	chr12:87232800-87233000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr12:87232800-87233000	Enhancers	Fetal Lung	lung

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