Variant report

Variant	rs2340943
Chromosome Location	chr14:55518007-55518008
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	EP300	chr14:55517997-55519067	H1-hESC	embryonic stem cell:	n/a	chr14:55518580-55518596 chr14:55518587-55518596 chr14:55518608-55518617 chr14:55518391-55518407
2	POLR2A	chr14:55517990-55519544	GM12891	blood:	n/a	n/a
3	REST	chr14:55517873-55519303	H1-neurons	neurons:	n/a	chr14:55518616-55518629 chr14:55518404-55518422 chr14:55518395-55518413
4	MYBL2	chr14:55517919-55518965	HepG2	liver:	n/a	n/a
5	TCF12	chr14:55517913-55519040	ECC-1	luminal epithelium:	n/a	n/a
6	MAX	chr14:55517859-55518798	GM12878	blood:	n/a	chr14:55518309-55518318
7	MAX	chr14:55517440-55519135	A549	lung:	n/a	chr14:55518309-55518318
8	HEY1	chr14:55517949-55519118	HepG2	liver:	n/a	chr14:55518793-55518802 chr14:55518933-55518948 chr14:55518791-55518800
9	YY1	chr14:55517988-55519014	HepG2	liver:	n/a	chr14:55518240-55518254 chr14:55518578-55518592 chr14:55518584-55518598 chr14:55518310-55518324 chr14:55518344-55518353 chr14:55518583-55518597
10	POLR2A	chr14:55517822-55519003	A549	lung:	n/a	n/a
11	POLR2A	chr14:55516344-55520058	GM12891	blood:	n/a	n/a
12	POLR2A	chr14:55517803-55519645	SK-N-SH	brain:	n/a	n/a
13	TRIM28	chr14:55517898-55518739	K562	blood:	n/a	n/a
14	MYBL2	chr14:55517849-55518727	HepG2	liver:	n/a	n/a
15	ELF1	chr14:55517944-55518591	K562	blood:	n/a	chr14:55518344-55518353 chr14:55518578-55518590
16	BHLHE40	chr14:55517925-55519144	GM12878	blood:	n/a	n/a
17	REST	chr14:55517961-55518307	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr14:55517512-55521594	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr14:55518004-55518839	GM12891	blood:	n/a	n/a
20	POLR2A	chr14:55517913-55519043	Gliobla	brain:	n/a	n/a
21	POLR2A	chr14:55517927-55519085	HL-60	blood:	n/a	n/a
22	POLR2A	chr14:55517474-55518918	U87	brain:	n/a	n/a
23	POLR2A	chr14:55517798-55519289	SK-N-MC	brain:	n/a	n/a
24	RXRA	chr14:55517993-55518403	GM12878	blood:	n/a	chr14:55518375-55518395 chr14:55518367-55518376 chr14:55518241-55518261 chr14:55518214-55518234
25	RAD21	chr14:55517981-55518574	ECC-1	luminal epithelium:	n/a	chr14:55518295-55518309 chr14:55518151-55518165 chr14:55518380-55518394 chr14:55518215-55518234 chr14:55518297-55518311 chr14:55518289-55518302
26	CHD2	chr14:55517914-55519059	K562	blood:	n/a	n/a
27	POLR2A	chr14:55517870-55519603	GM12891	blood:	n/a	n/a
28	CTCF	chr14:55517890-55518853	MCF-7	breast:	n/a	chr14:55518214-55518232 chr14:55518381-55518394 chr14:55518288-55518301 chr14:55518288-55518297 chr14:55518241-55518254 chr14:55518298-55518311 chr14:55518217-55518226 chr14:55518391-55518404 chr14:55518378-55518391
29	RAD21	chr14:55517853-55518593	MCF-7	breast:	n/a	chr14:55518295-55518309 chr14:55518151-55518165 chr14:55518380-55518394 chr14:55518215-55518234 chr14:55518297-55518311 chr14:55518289-55518302
30	YY1	chr14:55517983-55518573	SK-N-SH_RA	brain:	n/a	chr14:55518240-55518254 chr14:55518310-55518324 chr14:55518344-55518353
31	HEY1	chr14:55517901-55519110	HepG2	liver:	n/a	chr14:55518793-55518802 chr14:55518933-55518948 chr14:55518791-55518800
32	POLR2A	chr14:55517268-55519371	PANC-1	pancreas:	n/a	n/a
33	MAX	chr14:55517933-55519129	K562	blood:	n/a	chr14:55518309-55518318
34	STAT1	chr14:55517904-55518801	GM12878	blood:	n/a	chr14:55518329-55518341
35	HCFC1	chr14:55517820-55519083	K562	blood:	n/a	n/a
36	POLR2A	chr14:55517469-55519316	HUVEC	blood vessel:	n/a	n/a
37	SIN3AK20	chr14:55517976-55518814	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr14:55517937-55518825	HCT-116	colon:	n/a	chr14:55518214-55518232 chr14:55518381-55518394 chr14:55518288-55518301 chr14:55518288-55518297 chr14:55518241-55518254 chr14:55518298-55518311 chr14:55518217-55518226 chr14:55518391-55518404 chr14:55518378-55518391
39	SMC3	chr14:55517949-55519273	Hela-S3	cervix:	n/a	chr14:55518216-55518230
40	POU2F2	chr14:55517960-55518944	GM12878	blood:	n/a	n/a
41	TAF1	chr14:55517975-55519182	H1-neurons	neurons:	n/a	n/a
42	POLR2A	chr14:55517910-55519181	PFSK-1	brain:	n/a	n/a
43	REST	chr14:55517989-55518860	U87	brain:	n/a	chr14:55518616-55518629 chr14:55518404-55518422 chr14:55518395-55518413
44	EP300	chr14:55517988-55518518	T-47D	breast:	n/a	chr14:55518391-55518407
45	PAX5	chr14:55517978-55518994	GM12878	blood:	n/a	chr14:55518589-55518607
46	POLR2A	chr14:55517721-55519078	HepG2	liver:	n/a	n/a
47	CHD2	chr14:55517704-55519218	GM12878	blood:	n/a	n/a
48	FOXM1	chr14:55517846-55518989	GM12878	blood:	n/a	n/a
49	POLR2A	chr14:55517818-55519125	PANC-1	pancreas:	n/a	n/a
50	USF2	chr14:55517863-55518245	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:55517347..55519818-chr14:55736283..55739378,3	MCF-7	breast:
2	chr14:55517037..55520851-chr14:55594266..55601656,13	MCF-7	breast:
3	chr14:55517973..55518595-chr4:39460089..39460604,2	NB4	blood:
4	chr14:55368105..55371463-chr14:55516987..55520396,7	MCF-7	breast:
5	chr14:55516892..55519791-chr14:55737278..55740152,4	K562	blood:
6	chr14:55491083..55496744-chr14:55514437..55523536,23	MCF-7	breast:
7	chr14:55491921..55500295-chr14:55515389..55520812,24	K562	blood:
8	chr14:55491992..55498342-chr14:55515529..55520367,21	K562	blood:
9	chr14:55516908..55519746-chr14:55654326..55658338,3	K562	blood:
10	chr14:55517345..55520488-chr14:55656247..55658381,3	K562	blood:
11	chr14:55517047..55520032-chr14:55601675..55604188,2	MCF-7	breast:
12	chr14:54906668..54909344-chr14:55516272..55518741,3	K562	blood:
13	chr14:55490790..55495805-chr14:55515486..55522658,19	MCF-7	breast:
14	chr14:55516981..55523073-chr14:55594365..55600344,10	MCF-7	breast:
15	chr14:55367425..55371142-chr14:55516489..55521777,7	MCF-7	breast:
16	chr1:24069447..24070358-chr14:55517586..55518557,2	Hela-S3	cervix:
17	chr12:120314625..120315526-chr14:55517585..55518582,2	Hela-S3	cervix:

Variant related genes	Relation type
MAPK1IP1L	TF binding region
ENSG00000198554	Chromatin interaction
ENSG00000131979	Chromatin interaction
ENSG00000100528	Chromatin interaction
ENSG00000178974	Chromatin interaction
ENSG00000163682	Chromatin interaction
ENSG00000126787	Chromatin interaction
ENSG00000180008	Chromatin interaction
ENSG00000122966	Chromatin interaction
ENSG00000131981	Chromatin interaction
ENSG00000258413	Chromatin interaction
ENSG00000011007	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11158030	0.81[ASN][1000 genomes]
rs11158031	0.81[ASN][1000 genomes]
rs11622128	0.92[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs11625204	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11626816	0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs11627884	0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs11845087	0.83[ASN][1000 genomes]
rs11849878	0.83[ASN][1000 genomes]
rs11851178	0.82[ASN][1000 genomes]
rs1187873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1187874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1187876	0.84[CHB][hapmap]
rs1187878	0.80[ASN][1000 genomes]
rs1212641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17128128	0.82[ASN][1000 genomes]
rs17128132	0.82[ASN][1000 genomes]
rs17128145	0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1952085	0.82[ASN][1000 genomes]
rs2147963	0.85[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55843949	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60805089	0.82[ASN][1000 genomes]
rs61178993	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6573000	0.85[ASN][1000 genomes]
rs66962212	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66999765	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67652508	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67870023	0.83[ASN][1000 genomes]
rs7141975	0.85[ASN][1000 genomes]
rs7149965	0.82[ASN][1000 genomes]
rs7151431	0.82[ASN][1000 genomes]
rs7157678	0.83[ASN][1000 genomes]
rs7494066	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8015165	0.83[ASN][1000 genomes]
rs8016295	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9671895	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932970	chr14:55326559-55532749	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2340943	MAPK1IP1L	cis	Cerebellum	GTEx
rs2340943	C14orf32	Cis_1M	lymphoblastoid	RTeQTL
rs2340943	FBXO34	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55516800-55519600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr14:55517400-55519200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr14:55517400-55519400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:55517600-55518200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr14:55517600-55518200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr14:55517600-55518200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr14:55517600-55518200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr14:55517600-55518200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr14:55517600-55518200	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr14:55517600-55518200	Flanking Active TSS	Colonic Mucosa	Colon
11	chr14:55517600-55518200	Flanking Active TSS	Colon Smooth Muscle	Colon
12	chr14:55517600-55518200	Flanking Active TSS	Fetal Brain Male	brain
13	chr14:55517600-55518200	Flanking Active TSS	Fetal Muscle Trunk	muscle
14	chr14:55517600-55518200	Flanking Active TSS	Fetal Muscle Leg	muscle
15	chr14:55517600-55518200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr14:55517600-55518200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr14:55517600-55518200	Flanking Active TSS	Dnd41	blood
18	chr14:55517600-55518200	Flanking Active TSS	NHEK	skin
19	chr14:55517600-55518200	Flanking Active TSS	Osteobl	bone
20	chr14:55517600-55519000	Active TSS	Primary T cells from cord blood	blood
21	chr14:55517600-55519400	Active TSS	Pancreas	Pancrea
22	chr14:55517600-55519400	Active TSS	K562	blood
23	chr14:55517600-55519600	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr14:55517600-55519600	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr14:55517600-55519600	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr14:55517600-55519600	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr14:55517600-55519600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr14:55517600-55519600	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr14:55517600-55519800	Active TSS	H9 Cell Line	embryonic stem cell
30	chr14:55517600-55519800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr14:55517600-55519800	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr14:55517600-55520000	Active TSS	Fetal Brain Female	brain
33	chr14:55517800-55518200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr14:55517800-55518200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr14:55517800-55518200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr14:55517800-55518200	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr14:55517800-55518200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr14:55517800-55518200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr14:55517800-55518200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr14:55517800-55518200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr14:55517800-55518200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr14:55517800-55518200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr14:55517800-55518200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr14:55517800-55518200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr14:55517800-55518200	Flanking Active TSS	HSMMtube	muscle
46	chr14:55517800-55518200	Flanking Active TSS	HUVEC	blood vessel
47	chr14:55517800-55518200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr14:55517800-55518400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr14:55517800-55518400	Weak transcription	Small Intestine	intestine
50	chr14:55517800-55519000	Transcr. at gene 5' and 3'	Right Atrium	heart

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