Variant report

Variant	rs4930714
Chromosome Location	chr12:124067197-124067198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:124066463-124067550	A549	lung:	n/a	n/a
2	SMC3	chr12:124066549-124067501	SK-N-SH	brain:	n/a	n/a
3	BHLHE40	chr12:124066728-124067308	K562	blood:	n/a	n/a
4	RAD21	chr12:124066471-124067215	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr12:124066685-124067411	HepG2	liver:	n/a	n/a
6	TEAD4	chr12:124066638-124067245	K562	blood:	n/a	n/a
7	POLR2A	chr12:124066702-124067330	K562	blood:	n/a	n/a
8	CTCF	chr12:124067120-124067270	GM12866	blood:	n/a	n/a
9	CEBPB	chr12:124066710-124067259	K562	blood:	n/a	n/a
10	WRNIP1	chr12:124066757-124067251	GM12878	blood:	n/a	n/a
11	NR2F2	chr12:124066570-124067276	K562	blood:	n/a	n/a
12	MYC	chr12:124066675-124067282	K562	blood:	n/a	n/a
13	RAD21	chr12:124066637-124067201	HCT-116	colon:	n/a	n/a
14	CTCF	chr12:124067100-124067250	NHDF-neo	bronchial:	n/a	n/a
15	MYC	chr12:124066669-124067390	K562	blood:	n/a	n/a
16	CTCF	chr12:124066570-124067625	SK-N-SH	brain:	n/a	n/a
17	SMC3	chr12:124066659-124067299	HepG2	liver:	n/a	n/a
18	POLR2A	chr12:124066559-124067290	SK-N-MC	brain:	n/a	n/a
19	RFX5	chr12:124066807-124067236	K562	blood:	n/a	n/a
20	EP300	chr12:124066684-124067239	K562	blood:	n/a	n/a
21	RCOR1	chr12:124066760-124067377	K562	blood:	n/a	n/a
22	ZNF143	chr12:124066705-124067206	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr12:124066649-124067244	GM12878	blood:	n/a	n/a
24	CBX3	chr12:124066654-124067314	K562	blood:	n/a	n/a
25	RCOR1	chr12:124066669-124067300	K562	blood:	n/a	n/a
26	CTCF	chr12:124067100-124067250	AG04450	lung:	n/a	n/a
27	CTCF	chr12:124067140-124067290	HCM	heart:	n/a	n/a
28	MXI1	chr12:124066769-124067206	K562	blood:	n/a	n/a
29	CUX1	chr12:124066771-124067256	K562	blood:	n/a	n/a
30	TBL1XR1	chr12:124066698-124067370	K562	blood:	n/a	n/a
31	RAD21	chr12:124066653-124067249	HCT-116	colon:	n/a	n/a
32	CTCF	chr12:124067180-124067330	HMF	breast:	n/a	n/a
33	SIN3A	chr12:124066712-124067251	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr12:124067160-124067310	GM12865	blood:	n/a	n/a
35	RAD21	chr12:124066628-124067211	MCF-7	breast:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123846000..123850093-chr12:124067189..124070124,4	K562	blood:
2	chr12:123749254..123749803-chr12:124066367..124067369,3	MCF-7	breast:
3	chr12:124018073..124019067-chr12:124066380..124067358,3	MCF-7	breast:
4	chr12:123844989..123847500-chr12:124065839..124068689,2	K562	blood:
5	chr12:123868517..123870959-chr12:124065640..124068402,2	MCF-7	breast:
6	chr12:123846861..123850261-chr12:124066655..124071408,9	MCF-7	breast:
7	chr12:124061381..124063530-chr12:124065781..124068384,3	K562	blood:
8	chr12:124057277..124059073-chr12:124064975..124067218,3	MCF-7	breast:
9	chr12:123870366..123875219-chr12:124064500..124069174,6	K562	blood:
10	chr12:124060536..124063312-chr12:124065781..124067834,2	K562	blood:
11	chr12:124066647..124068350-chr12:124118155..124119898,2	K562	blood:
12	chr12:124018224..124020563-chr12:124065688..124070487,5	K562	blood:
13	chr12:123872778..123876196-chr12:124065295..124071344,6	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EIF2B1-1	chr12:124065613-124067714	XLOC_010229
2	lnc-EIF2B1-1	chr12:124066709-124068936	NONHSAT031599
3	lnc-EIF2B1-1	chr12:124065632-124067714	NR_110049

No data

Variant related genes	Relation type
TMED2	TF binding region
ENSG00000256092	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000188026	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000183955	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10161548	0.81[ASN][1000 genomes]
rs1050443	0.92[CEU][hapmap]
rs1050448	0.88[CEU][hapmap];0.86[MEX][hapmap]
rs1056132	0.83[EUR][1000 genomes]
rs1057879	1.00[JPT][hapmap]
rs10773019	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs10773020	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs10846530	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs10846532	0.81[ASN][1000 genomes]
rs11057297	1.00[JPT][hapmap]
rs11057299	0.81[ASN][1000 genomes]
rs11057300	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057304	0.81[ASN][1000 genomes]
rs11057310	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs11057312	0.88[CHD][hapmap]
rs12231444	0.81[ASN][1000 genomes]
rs12308953	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs12309685	0.86[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs12313119	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs12809479	0.83[ASN][1000 genomes]
rs12809853	0.95[CEU][hapmap]
rs15587	0.92[CEU][hapmap]
rs16917551	0.83[EUR][1000 genomes]
rs2292702	0.88[CHD][hapmap]
rs2333831	1.00[JPT][hapmap]
rs2707	0.81[ASN][1000 genomes]
rs3204541	0.92[CEU][hapmap];0.86[MEX][hapmap]
rs34369761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35064645	0.83[EUR][1000 genomes]
rs36002329	0.81[EUR][1000 genomes]
rs3704	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs3850952	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930712	0.83[EUR][1000 genomes]
rs4930713	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61154946	0.81[ASN][1000 genomes]
rs66494087	0.82[EUR][1000 genomes]
rs7298287	0.86[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs7309292	0.83[EUR][1000 genomes]
rs7313207	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs73414223	0.81[ASN][1000 genomes]
rs7358562	0.86[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs786447	1.00[JPT][hapmap]
rs786454	0.81[ASN][1000 genomes]
rs7953876	0.82[EUR][1000 genomes]
rs7971323	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7972380	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973766	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7979561	0.81[EUR][1000 genomes]
rs9919	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4930714	TCTN2	cis	cerebellum	SCAN
rs4930714	EIF2B1	Cis_1M	lymphoblastoid	RTeQTL
rs4930714	SIRT4	cis	cerebellum	SCAN
rs4930714	MPHOSPH9	cis	cerebellum	SCAN
rs4930714	ABCB9	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124055000-124067400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr12:124055200-124068000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:124055400-124067800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:124056000-124067800	Weak transcription	Lung	lung
5	chr12:124056200-124067200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:124056400-124067400	Weak transcription	HSMMtube	muscle
7	chr12:124059200-124067200	Weak transcription	Brain Germinal Matrix	brain
8	chr12:124059400-124067200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:124061200-124067200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:124065800-124067400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr12:124066400-124070000	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr12:124066600-124067200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr12:124066600-124067400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
14	chr12:124066600-124067600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr12:124066600-124067600	Enhancers	Fetal Muscle Leg	muscle
16	chr12:124066600-124067600	Enhancers	Fetal Stomach	stomach
17	chr12:124066600-124067600	Enhancers	Fetal Thymus	thymus
18	chr12:124066600-124067600	Enhancers	Small Intestine	intestine
19	chr12:124066600-124067800	Enhancers	Primary B cells from cord blood	blood
20	chr12:124066600-124067800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr12:124066600-124067800	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr12:124066600-124067800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr12:124066600-124067800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:124066600-124067800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr12:124066600-124067800	Enhancers	Placenta	Placenta
26	chr12:124066600-124067800	Enhancers	Pancreas	Pancrea
27	chr12:124066600-124068000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:124066600-124068000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:124066600-124068000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:124066600-124068000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:124066600-124068000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:124066600-124068200	Flanking Active TSS	Thymus	Thymus
33	chr12:124066600-124068200	Flanking Active TSS	Dnd41	blood
34	chr12:124066800-124067200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:124066800-124067200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr12:124066800-124067200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr12:124066800-124067200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:124066800-124067400	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr12:124066800-124067400	Enhancers	Brain Hippocampus Middle	brain
40	chr12:124066800-124067400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr12:124066800-124067400	Flanking Active TSS	A549	lung
42	chr12:124066800-124067400	Flanking Active TSS	K562	blood
43	chr12:124066800-124067600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:124066800-124067600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:124066800-124067600	Enhancers	Fetal Kidney	kidney
46	chr12:124066800-124067600	Enhancers	Ovary	ovary
47	chr12:124066800-124067600	Flanking Active TSS	Hela-S3	cervix
48	chr12:124066800-124067800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:124066800-124067800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr12:124066800-124067800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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