Variant report

Variant	rs117769037
Chromosome Location	chr12:50793978-50793979
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:61)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr12:50793716-50795503	MCF-7	breast:	n/a	n/a
2	GTF3C2	chr12:50793568-50794516	Hela-S3	cervix:	n/a	n/a
3	SIX5	chr12:50793795-50795541	A549	lung:	n/a	n/a
4	HCFC1	chr12:50793659-50796979	Hela-S3	cervix:	n/a	n/a
5	RUNX3	chr12:50793945-50795542	GM12878	blood:	n/a	n/a
6	CUX1	chr12:50793956-50794788	K562	blood:	n/a	n/a
7	NR2F2	chr12:50793846-50795251	K562	blood:	n/a	n/a
8	POLR2A	chr12:50793897-50795206	PFSK-1	brain:	n/a	n/a
9	TCF12	chr12:50793865-50795875	A549	lung:	n/a	n/a
10	SREBP1	chr12:50793715-50796327	GM12878	blood:	n/a	n/a
11	MYBL2	chr12:50793918-50795238	HepG2	liver:	n/a	n/a
12	CHD1	chr12:50793862-50797087	IMR90	lung:	n/a	n/a
13	POLR2A	chr12:50793926-50795923	MCF10A-Er-Src	breast:	n/a	n/a
14	REST	chr12:50793907-50795139	A549	lung:	n/a	chr12:50794936-50794946
15	NFIC	chr12:50793970-50794806	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:50793905-50795962	MCF10A-Er-Src	breast:	n/a	n/a
17	MXI1	chr12:50793934-50795945	SK-N-SH	brain:	n/a	n/a
18	TBP	chr12:50793877-50795088	Hela-S3	cervix:	n/a	n/a
19	GABPA	chr12:50793962-50795208	HL-60	blood:	n/a	n/a
20	JUND	chr12:50793721-50795977	SK-N-SH	brain:	n/a	chr12:50795851-50795860
21	POLR2A	chr12:50793938-50795249	HUVEC	blood vessel:	n/a	n/a
22	TEAD4	chr12:50793910-50795861	K562	blood:	n/a	n/a
23	GABPA	chr12:50793827-50795481	A549	lung:	n/a	n/a
24	POLR2A	chr12:50793926-50795301	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr12:50793831-50795216	SK-N-MC	brain:	n/a	n/a
26	TCF7L2	chr12:50793974-50794677	HEK293	kidney:	n/a	n/a
27	FOSL2	chr12:50793912-50795226	A549	lung:	n/a	n/a
28	TBL1XR1	chr12:50793939-50795053	K562	blood:	n/a	n/a
29	SP1	chr12:50793912-50795288	A549	lung:	n/a	chr12:50795132-50795142 chr12:50795131-50795143 chr12:50795131-50795143 chr12:50795128-50795142 chr12:50795132-50795141
30	CEBPB	chr12:50793943-50794774	GM12878	blood:	n/a	n/a
31	JUND	chr12:50793873-50795266	GM12878	blood:	n/a	n/a
32	SIN3AK20	chr12:50793922-50795308	MCF-7	breast:	n/a	n/a
33	BRCA1	chr12:50793898-50795115	Hela-S3	cervix:	n/a	n/a
34	JUND	chr12:50793931-50795654	K562	blood:	n/a	n/a
35	POLR2A	chr12:50793967-50795582	SK-N-MC	brain:	n/a	n/a
36	GABPA	chr12:50793856-50795422	A549	lung:	n/a	n/a
37	ARID3A	chr12:50793878-50794885	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:50793961-50794011	GM12891	blood:	n/a
2	chr12:50793961-50794011	NHDF-neo	bronchial:	n/a
3	chr12:50793961-50794011	GM06990	blood:	n/a
4	chr12:50793961-50794011	PFSK-1	brain:	n/a
5	chr12:50793961-50794011	PANC-1	pancreas:	n/a
6	chr12:50793961-50794011	SK-N-SH	brain:	n/a
7	chr12:50793961-50794011	RPTEC	kidney:	n/a
8	chr12:50793961-50794011	PrEC	prostate:	n/a
9	chr12:50793961-50794011	SK-N-MC	brain:	n/a
10	chr12:50793961-50794011	HAEpiC	amniotic membrane:	n/a
11	chr12:50793961-50794011	GM12892	blood:	n/a
12	chr12:50793961-50794011	ECC-1	luminal epithelium:	n/a
13	chr12:50793961-50794011	HPAEpiC	pulmonary alveolar:	n/a
14	chr12:50793961-50794011	HNPCEpiC	eye:	n/a
15	chr12:50793961-50794011	HIPEpiC	eye:	n/a
16	chr12:50793961-50794011	HRPEpiC	eye:	n/a
17	chr12:50793961-50794011	LNCaP	prostate:	n/a
18	chr12:50793961-50794011	HCPEpiC	choroid plexus:	n/a
19	chr12:50793961-50794011	A549	lung:	n/a
20	chr12:50793961-50794011	SK-N-SH_RA	brain:	n/a
21	chr12:50793961-50794011	AG09309	skin:	n/a
22	chr12:50793961-50794011	K562	blood:	n/a
23	chr12:50793961-50794011	AG10803	skin:	n/a
24	chr12:50793961-50794011	AG04449	skin:	fetal
25	chr12:50793961-50794011	HepG2	liver:	n/a
26	chr12:50793961-50794011	AG09319	gingival:	n/a
27	chr12:50793961-50794011	HEEpiC	esophagus:	n/a
28	chr12:50793961-50794011	GM19239	blood:	n/a
29	chr12:50793961-50794011	HCF	heart:	n/a
30	chr12:50793961-50794011	U87	brain:	n/a
31	chr12:50793961-50794011	SAEC	small airway:	n/a
32	chr12:50793961-50794011	NH-A	brain:	n/a
33	chr12:50793961-50794011	ovcar-3	ovarian:	n/a
34	chr12:50793961-50794011	AoSMC	blood vessel:	n/a
35	chr12:50793961-50794011	Jurkat	blood:	n/a
36	chr12:50793961-50794011	CMK	blood:	n/a
37	chr12:50793961-50794011	BE2_C	brain:	n/a
38	chr12:50793961-50794011	HCM	heart:	n/a
39	chr12:50793961-50794011	HCT-116	colon:	n/a
40	chr12:50793961-50794011	HMEC	breast:	n/a
41	chr12:50793961-50794011	MCF10A-Er-Src	breast:	n/a
42	chr12:50793961-50794011	HUVEC	blood vessel:	n/a
43	chr12:50793961-50794011	HRE	kidney:	n/a
44	chr12:50793961-50794011	HL-60	blood:	n/a
45	chr12:50793961-50794011	GM12878	blood:	n/a
46	chr12:50793961-50794011	Caco-2	colon:	n/a
47	chr12:50793961-50794011	SKMC	muscle:	n/a
48	chr12:50793961-50794011	NT2-D1	testis:	n/a
49	chr12:50793961-50794011	ProgFib	skin:	n/a
50	chr12:50793961-50794011	BJ	skin:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr12:50416797..50419367-chr12:50793748..50795984,3	K562	blood:
2	chr12:50677350..50679861-chr12:50792501..50795030,2	K562	blood:
3	chr12:50495184..50497904-chr12:50792002..50794811,2	K562	blood:
4	chr12:50560048..50562244-chr12:50793488..50796318,2	MCF-7	breast:
5	chr12:50793053..50795901-chr12:51566225..51568182,2	K562	blood:
6	chr12:50504921..50507290-chr12:50793420..50795913,2	K562	blood:
7	chr12:50614841..50617436-chr12:50793138..50795396,3	K562	blood:
8	chr12:50793597..50795392-chr12:51156771..51159161,2	MCF-7	breast:
9	chr12:50611453..50613308-chr12:50792675..50795177,2	K562	blood:
10	chr12:50792642..50794335-chr12:50796337..50798839,2	MCF-7	breast:
11	chr12:50639732..50644182-chr12:50792343..50795361,4	K562	blood:
12	chr12:50614841..50617436-chr12:50793138..50796219,5	K562	blood:
13	chr12:50787607..50792856-chr12:50793045..50797935,10	K562	blood:
14	chr12:50758172..50761780-chr12:50791230..50796188,4	K562	blood:
15	chr12:50744030..50745748-chr12:50793472..50795953,2	K562	blood:

No data

Variant related genes	Relation type
LARP4	TF binding region
FAM186A	TF binding region
LARP4	CpG island
FAM186A	CpG island
ENSG00000203433	Chromatin interaction
ENSG00000050405	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000161800	Chromatin interaction
ENSG00000244266	Chromatin interaction
ENSG00000167588	Chromatin interaction
ENSG00000135457	Chromatin interaction
ENSG00000257531	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000185958	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1053667	chr12:50679039-50801752	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1054480	chr12:50691039-50859665	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv1041563	chr12:50705715-50861699	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1049665	chr12:50705715-50871542	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv899076	chr12:50770291-50869589	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
8	nsv469376	chr12:50792846-50856613	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
9	nsv558841	chr12:50792846-50856613	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
10	nsv470291	chr12:50792846-50858820	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50781800-50794000	Weak transcription	Fetal Kidney	kidney
2	chr12:50782000-50794000	Weak transcription	Fetal Heart	heart
3	chr12:50782800-50794200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:50785000-50794000	Weak transcription	HUVEC	blood vessel
5	chr12:50790200-50794000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:50790600-50794000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:50790600-50794200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:50790800-50794000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:50790800-50794000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:50790800-50794200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:50791000-50794000	Weak transcription	A549	lung
12	chr12:50791000-50794000	Weak transcription	NHDF-Ad	bronchial
13	chr12:50791200-50794000	Weak transcription	HMEC	breast
14	chr12:50791400-50794000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:50791400-50794200	Weak transcription	Placenta	Placenta
16	chr12:50793600-50794400	Flanking Active TSS	Dnd41	blood
17	chr12:50793600-50796800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:50793800-50794000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:50793800-50794000	Enhancers	Primary B cells from cord blood	blood
20	chr12:50793800-50794000	Enhancers	Primary B cells from peripheral blood	blood
21	chr12:50793800-50794000	Enhancers	Primary T cells from cord blood	blood
22	chr12:50793800-50794000	Enhancers	Primary hematopoietic stem cells	blood
23	chr12:50793800-50794000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr12:50793800-50794000	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr12:50793800-50794000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr12:50793800-50794000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:50793800-50794000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:50793800-50794000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:50793800-50794000	Enhancers	Muscle Satellite Cultured Cells	--
30	chr12:50793800-50794000	Enhancers	Liver	Liver
31	chr12:50793800-50794000	Enhancers	Brain Substantia Nigra	brain
32	chr12:50793800-50794000	Enhancers	Colon Smooth Muscle	Colon
33	chr12:50793800-50794000	Enhancers	Fetal Intestine Small	intestine
34	chr12:50793800-50794000	Enhancers	Fetal Thymus	thymus
35	chr12:50793800-50794000	Enhancers	Osteobl	bone
36	chr12:50793800-50794200	Enhancers	Placenta Amnion	Placenta Amnion
37	chr12:50793800-50794400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:50793800-50794800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:50793800-50794800	Active TSS	HepG2	liver
40	chr12:50793800-50795000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:50793800-50795400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:50793800-50795400	Active TSS	Duodenum Mucosa	Duodenum
43	chr12:50793800-50795400	Active TSS	Fetal Brain Female	brain
44	chr12:50793800-50796200	Active TSS	Brain Germinal Matrix	brain
45	chr12:50793800-50796200	Active TSS	NHEK	skin
46	chr12:50793800-50796400	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr12:50793800-50796400	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr12:50793800-50796400	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr12:50793800-50796600	Active TSS	Hela-S3	cervix
50	chr12:50793800-50797000	Active TSS	iPS-15b Cell Line	embryonic stem cell

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