Variant report

Variant	rs12323555
Chromosome Location	chr14:78083548-78083549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr14:78082903-78083690	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr14:78082019-78083667	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr14:78082706-78083666	K562	blood:	n/a	n/a
4	CTCF	chr14:78083368-78083553	GM12892	blood:	n/a	n/a
5	SMC3	chr14:78082836-78083642	Hela-S3	cervix:	n/a	n/a
6	IRF3	chr14:78083042-78083605	Hela-S3	cervix:	n/a	chr14:78083355-78083369 chr14:78083216-78083225 chr14:78083068-78083082
7	MAZ	chr14:78082366-78083602	Hela-S3	cervix:	n/a	chr14:78083069-78083079
8	CTCF	chr14:78083400-78083550	HRPEpiC	eye:	n/a	n/a
9	CTCF	chr14:78083460-78083610	Hela-S3	cervix:	n/a	n/a
10	HA-E2F1	chr14:78082606-78083589	Hela-S3	cervix:	n/a	chr14:78082972-78082982 chr14:78082969-78082979 chr14:78083216-78083225
11	GTF2F1	chr14:78082928-78083654	Hela-S3	cervix:	n/a	n/a
12	MAZ	chr14:78082699-78083597	HepG2	liver:	n/a	chr14:78083069-78083079
13	SIN3A	chr14:78082244-78083644	H1-hESC	embryonic stem cell:	n/a	chr14:78082726-78082737 chr14:78082931-78082940
14	RAD21	chr14:78083311-78083595	SK-N-SH_RA	brain:	n/a	n/a
15	CTCF	chr14:78083400-78083550	HPF	lung:	n/a	n/a
16	EP300	chr14:78082925-78083624	K562	blood:	n/a	chr14:78082970-78082979
17	CTCF	chr14:78083420-78083570	NHEK	skin:	n/a	n/a
18	CTCF	chr14:78082856-78083644	GM12878	blood:	n/a	chr14:78083350-78083363
19	CTCF	chr14:78083378-78083551	GM10248	blood:	n/a	n/a
20	SP1	chr14:78082978-78083636	GM12878	blood:	n/a	chr14:78083215-78083236 chr14:78083068-78083080 chr14:78083352-78083366 chr14:78083069-78083078 chr14:78083068-78083080 chr14:78083070-78083079 chr14:78083069-78083079 chr14:78083355-78083367 chr14:78083065-78083079 chr14:78083403-78083410 chr14:78083000-78083010
21	CTCF	chr14:78083350-78083564	GM12891	blood:	n/a	chr14:78083350-78083363
22	MYC	chr14:78082791-78083810	MCF10A-Er-Src	breast:	n/a	chr14:78083657-78083673 chr14:78083069-78083079
23	MYC	chr14:78082535-78083671	Hela-S3	cervix:	n/a	chr14:78083069-78083079
24	CTCF	chr14:78083400-78083550	AG04449	skin:	n/a	n/a
25	E2F6	chr14:78082816-78083673	H1-hESC	embryonic stem cell:	n/a	chr14:78082972-78082982 chr14:78082969-78082979 chr14:78083216-78083225
26	BHLHE40	chr14:78082876-78083607	K562	blood:	n/a	chr14:78082959-78082975 chr14:78082965-78082981
27	MAZ	chr14:78082238-78083674	GM12878	blood:	n/a	chr14:78083657-78083673 chr14:78083069-78083079
28	SP1	chr14:78082809-78083551	GM12878	blood:	n/a	chr14:78083215-78083236 chr14:78083068-78083080 chr14:78083352-78083366 chr14:78083069-78083078 chr14:78083068-78083080 chr14:78083070-78083079 chr14:78083069-78083079 chr14:78083355-78083367 chr14:78083065-78083079 chr14:78083403-78083410 chr14:78083000-78083010
29	CTCF	chr14:78083400-78083550	HPAF	blood vessel:	n/a	n/a
30	CTCF	chr14:78083420-78083570	HRE	kidney:	n/a	n/a
31	MYC	chr14:78082652-78083650	NB4	blood:	n/a	chr14:78083069-78083079
32	TBL1XR1	chr14:78082976-78083593	K562	blood:	n/a	n/a
33	MAZ	chr14:78082588-78083752	K562	blood:	n/a	chr14:78083657-78083673 chr14:78083069-78083079
34	SP1	chr14:78082892-78083641	HepG2	liver:	n/a	chr14:78083215-78083236 chr14:78083068-78083080 chr14:78083352-78083366 chr14:78083069-78083078 chr14:78083068-78083080 chr14:78083070-78083079 chr14:78083069-78083079 chr14:78083355-78083367 chr14:78083065-78083079 chr14:78083403-78083410 chr14:78083000-78083010
35	POLR2A	chr14:78082747-78083624	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr14:78083332-78083591	K562	blood:	n/a	n/a
37	POLR2A	chr14:78082654-78083815	GM12878	blood:	n/a	n/a
38	NRF1	chr14:78082938-78083568	GM12878	blood:	n/a	n/a
39	PML	chr14:78082602-78083769	GM12878	blood:	n/a	chr14:78083261-78083269
40	EP300	chr14:78082884-78083635	T-47D	breast:	n/a	chr14:78082970-78082979
41	GABPA	chr14:78082729-78083610	SK-N-SH	brain:	n/a	n/a
42	MAX	chr14:78082810-78083637	GM12878	blood:	n/a	chr14:78083069-78083079
43	ELK1	chr14:78082814-78083598	Hela-S3	cervix:	n/a	chr14:78083020-78083029 chr14:78083020-78083029
44	SP1	chr14:78082794-78083716	H1-hESC	embryonic stem cell:	n/a	chr14:78083215-78083236 chr14:78083068-78083080 chr14:78083352-78083366 chr14:78083069-78083078 chr14:78083068-78083080 chr14:78083070-78083079 chr14:78083069-78083079 chr14:78083355-78083367 chr14:78083065-78083079 chr14:78083403-78083410 chr14:78083000-78083010
45	CTCF	chr14:78082840-78083582	IMR90	lung:	n/a	chr14:78083350-78083363
46	FOS	chr14:78083015-78083558	GM12878	blood:	n/a	n/a
47	POLR2A	chr14:78083300-78083602	Hela-S3	cervix:	n/a	n/a
48	MAX	chr14:78082755-78083622	SK-N-SH	brain:	n/a	chr14:78083069-78083079
49	CTCF	chr14:78083540-78083690	GM12868	blood:	n/a	n/a
50	POLR2A	chr14:78081616-78083700	IMR90	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr14:78083524-78083574	HCPEpiC	choroid plexus:	n/a
2	chr14:78083524-78083574	HNPCEpiC	eye:	n/a
3	chr14:78083524-78083574	SKMC	muscle:	n/a
4	chr14:78083524-78083574	CMK	blood:	n/a
5	chr14:78083524-78083574	MCF10A-Er-Src	breast:	n/a
6	chr14:78083524-78083574	HEEpiC	esophagus:	n/a
7	chr14:78083524-78083574	MCF-7	breast:	n/a
8	chr14:78083524-78083574	HPAEpiC	pulmonary alveolar:	n/a
9	chr14:78083524-78083574	BJ	skin:	n/a
10	chr14:78083524-78083574	Hepatocyte	liver:	n/a
11	chr14:78083524-78083574	HIPEpiC	eye:	n/a
12	chr14:78083524-78083574	H1-hESC	embryonic stem cell:	embryo
13	chr14:78083524-78083574	PrEC	prostate:	n/a
14	chr14:78083524-78083574	HMEC	breast:	n/a
15	chr14:78083524-78083574	RPTEC	kidney:	n/a
16	chr14:78083524-78083574	GM19239	blood:	n/a
17	chr14:78083524-78083574	NT2-D1	testis:	n/a
18	chr14:78083524-78083574	AoSMC	blood vessel:	n/a
19	chr14:78083524-78083574	SK-N-SH_RA	brain:	n/a
20	chr14:78083524-78083574	LNCaP	prostate:	n/a
21	chr14:78083524-78083574	NHBE	bronchial:	n/a
22	chr14:78083524-78083574	SK-N-MC	brain:	n/a
23	chr14:78083524-78083574	HUVEC	blood vessel:	n/a
24	chr14:78083524-78083574	Jurkat	blood:	n/a
25	chr14:78083524-78083574	U87	brain:	n/a
26	chr14:78083524-78083574	GM06990	blood:	n/a
27	chr14:78083524-78083574	HEK293	kidney:	embryo
28	chr14:78083524-78083574	BE2_C	brain:	n/a
29	chr14:78083524-78083574	HCT-116	colon:	n/a
30	chr14:78083524-78083574	NH-A	brain:	n/a
31	chr14:78083524-78083574	HCF	heart:	n/a
32	chr14:78083524-78083574	SAEC	small airway:	n/a
33	chr14:78083524-78083574	ProgFib	skin:	n/a
34	chr14:78083524-78083574	HCM	heart:	n/a
35	chr14:78083524-78083574	GM12892	blood:	n/a
36	chr14:78083524-78083574	HepG2	liver:	n/a
37	chr14:78083524-78083574	GM12891	blood:	n/a
38	chr14:78083524-78083574	HRE	kidney:	n/a
39	chr14:78083524-78083574	ECC-1	luminal epithelium:	n/a
40	chr14:78083524-78083574	HL-60	blood:	n/a
41	chr14:78083524-78083574	Hela-S3	cervix:	n/a
42	chr14:78083524-78083574	NB4	blood:	n/a
43	chr14:78083524-78083574	GM12878	blood:	n/a
44	chr14:78083524-78083574	PFSK-1	brain:	n/a
45	chr14:78083524-78083574	SK-N-SH	brain:	n/a
46	chr14:78083524-78083574	HRPEpiC	eye:	n/a
47	chr14:78083524-78083574	IMR90	lung:	fetal
48	chr14:78083524-78083574	AG09319	gingival:	n/a
49	chr14:78083524-78083574	K562	blood:	n/a
50	chr14:78083524-78083574	AG09309	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:77786606..77788826-chr14:78082183..78084255,2	K562	blood:
2	chr14:77782973..77788435-chr14:78081530..78084931,5	MCF-7	breast:
3	chr14:77925306..77928562-chr14:78081993..78085089,3	MCF-7	breast:
4	chr14:78081876..78084095-chr14:78119324..78121053,2	MCF-7	breast:
5	chr14:77922506..77924938-chr14:78082363..78084357,2	MCF-7	breast:
6	chr14:78081719..78084170-chr17:57917300..57920054,2	MCF-7	breast:

Variant related genes	Relation type
SPTLC2	TF binding region
SPTLC2	CpG island
ENSG00000100591	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000258668	Chromatin interaction
ENSG00000009830	Chromatin interaction
ENSG00000100577	Chromatin interaction
ENSG00000151445	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs176910	0.81[ASN][1000 genomes]
rs176913	0.82[ASN][1000 genomes]
rs176917	0.80[ASN][1000 genomes]
rs2299926	0.93[ASN][1000 genomes]
rs34278364	0.93[ASN][1000 genomes]
rs35503744	0.93[ASN][1000 genomes]
rs60287878	0.94[ASN][1000 genomes]
rs7156939	0.93[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	nsv832835	chr14:77906706-78095207	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78080200-78083800	Active TSS	GM12878-XiMat	blood
2	chr14:78081200-78083600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr14:78081400-78083600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr14:78081400-78083600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr14:78081400-78083600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr14:78081400-78083600	Active TSS	Ovary	ovary
7	chr14:78081400-78083600	Active TSS	Right Atrium	heart
8	chr14:78081400-78083600	Active TSS	HSMMtube	muscle
9	chr14:78081400-78083600	Active TSS	NHLF	lung
10	chr14:78081400-78083800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr14:78081400-78083800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr14:78081400-78083800	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr14:78081600-78083600	Active TSS	Muscle Satellite Cultured Cells	--
14	chr14:78081600-78083600	Active TSS	Fetal Kidney	kidney
15	chr14:78081600-78083600	Active TSS	Psoas Muscle	Psoas
16	chr14:78081600-78083600	Active TSS	Right Ventricle	heart
17	chr14:78081600-78083600	Active TSS	A549	lung
18	chr14:78081800-78083600	Active TSS	H1 Cell Line	embryonic stem cell
19	chr14:78081800-78083600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr14:78081800-78083600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr14:78081800-78083600	Active TSS	HSMM	muscle
22	chr14:78081800-78083600	Active TSS	Osteobl	bone
23	chr14:78082000-78083600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:78082000-78083600	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr14:78082000-78083600	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr14:78082000-78083600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr14:78082000-78083600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr14:78082000-78083600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr14:78082000-78083600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr14:78082000-78083600	Active TSS	Colonic Mucosa	Colon
31	chr14:78082000-78083600	Active TSS	Pancreas	Pancrea
32	chr14:78082000-78083600	Active TSS	HMEC	breast
33	chr14:78082000-78083800	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr14:78082000-78083800	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr14:78082000-78083800	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr14:78082000-78083800	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr14:78082000-78083800	Active TSS	Hela-S3	cervix
38	chr14:78082200-78083600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr14:78082200-78083600	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr14:78082200-78083600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr14:78082200-78083600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr14:78082200-78083600	Active TSS	Fetal Lung	lung
43	chr14:78082200-78083800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr14:78082200-78083800	Active TSS	Brain Anterior Caudate	brain
45	chr14:78082200-78083800	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr14:78082400-78083600	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr14:78082400-78083600	Active TSS	Brain Hippocampus Middle	brain
48	chr14:78082400-78083600	Active TSS	Brain Substantia Nigra	brain
49	chr14:78082400-78083600	Active TSS	Rectal Smooth Muscle	rectum
50	chr14:78082400-78083600	Active TSS	Thymus	Thymus

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