Variant report

Variant	rs316398
Chromosome Location	chr5:43038026-43038027
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	SUZ12	chr5:43036692-43038919	H1-hESC	embryonic stem cell:	n/a	n/a
2	POU2F2	chr5:43037916-43038609	GM12878	blood:	n/a	n/a
3	BCLAF1	chr5:43037805-43038494	GM12878	blood:	n/a	n/a
4	POLR2A	chr5:43037972-43038225	GM12878	blood:	n/a	n/a
5	MYC	chr5:43037870-43038361	K562	blood:	n/a	n/a
6	POLR2A	chr5:43037974-43038569	PBDE	blood:	n/a	n/a
7	BATF	chr5:43037953-43038319	GM12878	blood:	n/a	n/a
8	IRF1	chr5:43037895-43038416	K562	blood:	n/a	chr5:43038174-43038187 chr5:43038175-43038189 chr5:43038173-43038187 chr5:43038174-43038187 chr5:43038172-43038186 chr5:43038174-43038187 chr5:43038174-43038187 chr5:43038176-43038187 chr5:43038168-43038188
9	NFIC	chr5:43037852-43038380	GM12878	blood:	n/a	n/a
10	POLR2A	chr5:43037810-43038540	GM12878	blood:	n/a	n/a
11	ATF2	chr5:43037858-43038438	GM12878	blood:	n/a	n/a
12	ZMIZ1	chr5:43037980-43038042	K562	blood:	n/a	n/a
13	EP300	chr5:43037961-43038073	K562	blood:	n/a	chr5:43037963-43037973
14	FOXM1	chr5:43037931-43038615	GM12878	blood:	n/a	n/a
15	POLR2A	chr5:43037897-43039072	HUVEC	blood vessel:	n/a	n/a
16	FOXM1	chr5:43037827-43038882	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr5:43037911-43038369	GM12878	blood:	n/a	n/a
18	POLR2A	chr5:43036949-43038717	HL-60	blood:	n/a	n/a
19	PML	chr5:43037672-43038872	GM12878	blood:	n/a	chr5:43038426-43038434
20	RUNX3	chr5:43037804-43038917	GM12878	blood:	n/a	chr5:43038430-43038439 chr5:43038430-43038439
21	MEF2A	chr5:43037932-43038414	GM12878	blood:	n/a	chr5:43038128-43038143 chr5:43038127-43038143
22	TAF1	chr5:43037909-43038299	GM12878	blood:	n/a	n/a
23	POLR2A	chr5:43038026-43039068	HL-60	blood:	n/a	n/a
24	MAFK	chr5:43038024-43038415	K562	blood:	n/a	n/a
25	MTA3	chr5:43037959-43038617	GM12878	blood:	n/a	n/a
26	IRF1	chr5:43037978-43038387	K562	blood:	n/a	chr5:43038174-43038187 chr5:43038175-43038189 chr5:43038173-43038187 chr5:43038174-43038187 chr5:43038172-43038186 chr5:43038174-43038187 chr5:43038174-43038187 chr5:43038176-43038187 chr5:43038168-43038188
27	MEF2A	chr5:43037750-43038417	GM12878	blood:	n/a	chr5:43038128-43038143 chr5:43038127-43038143
28	RCOR1	chr5:43036862-43039162	IMR90	lung:	n/a	n/a
29	POLR2A	chr5:43036710-43039237	H1-neurons	neurons:	n/a	n/a
30	MTA3	chr5:43037784-43039044	GM12878	blood:	n/a	n/a
31	NFIC	chr5:43037818-43038829	GM12878	blood:	n/a	n/a
32	TEAD4	chr5:43037808-43039115	K562	blood:	n/a	n/a
33	RUNX3	chr5:43037818-43038916	GM12878	blood:	n/a	chr5:43038430-43038439 chr5:43038430-43038439
34	POLR2A	chr5:43037889-43039063	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr5:43037920-43038416	PANC-1	pancreas:	n/a	n/a
36	IRF1	chr5:43037929-43038600	K562	blood:	n/a	chr5:43038174-43038187 chr5:43038175-43038189 chr5:43038173-43038187 chr5:43038174-43038187 chr5:43038172-43038186 chr5:43038174-43038187 chr5:43038174-43038187 chr5:43038176-43038187 chr5:43038168-43038188
37	MEF2C	chr5:43037857-43038439	GM12878	blood:	n/a	chr5:43038128-43038143 chr5:43038128-43038143 chr5:43038127-43038143

No.	Distal block	Cell Line	Cell type
1	chr5:43029265..43030861-chr5:43036238..43038466,2	K562	blood:
2	chr5:43005892..43011349-chr5:43037590..43043804,20	K562	blood:
3	chr5:43034026..43036831-chr5:43037498..43040104,5	MCF-7	breast:
4	chr5:43013791..43017090-chr5:43037504..43040048,4	K562	blood:
5	chr5:42907582..42909644-chr5:43037324..43039921,2	K562	blood:
6	chr5:43016691..43021968-chr5:43036071..43044426,17	MCF-7	breast:
7	chr5:43014739..43026335-chr5:43034830..43045515,33	MCF-7	breast:
8	chr5:43013791..43016658-chr5:43037504..43040048,3	K562	blood:
9	chr5:43034726..43053192-chr5:43061725..43074206,66	K562	blood:
10	chr5:42967335..42969495-chr5:43037103..43039655,2	K562	blood:
11	chr5:43036901..43050217-chr5:43060442..43069391,53	MCF-7	breast:
12	chr5:43037720..43044659-chr5:43062293..43069444,31	K562	blood:
13	chr5:43036891..43039253-chr5:43074561..43077276,2	MCF-7	breast:
14	chr5:43005322..43013124-chr5:43037748..43043287,15	K562	blood:
15	chr5:43008478..43012422-chr5:43036002..43039064,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215068	TF binding region
ENSG00000272144	Chromatin interaction
ENSG00000271788	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000251131	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000251656	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10058374	0.81[JPT][hapmap]
rs10074873	0.81[JPT][hapmap]
rs1032434	0.82[ASN][1000 genomes]
rs10454865	0.85[ASN][1000 genomes]
rs10805667	0.80[JPT][hapmap]
rs10941607	0.81[JPT][hapmap]
rs10941608	0.82[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs11550285	0.81[ASN][1000 genomes]
rs11550286	0.80[ASN][1000 genomes]
rs11550287	0.80[ASN][1000 genomes]
rs11740797	0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs11742691	0.85[ASN][1000 genomes]
rs11748187	0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs11949817	0.82[ASN][1000 genomes]
rs11956243	0.80[ASN][1000 genomes]
rs13155513	0.82[ASN][1000 genomes]
rs13173064	0.80[CHD][hapmap];0.82[ASN][1000 genomes]
rs13665	0.81[JPT][hapmap]
rs1532331	0.81[JPT][hapmap]
rs1574407	0.83[CEU][hapmap]
rs17301375	0.81[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs178415	0.83[CEU][hapmap]
rs2452831	0.82[ASN][1000 genomes]
rs316404	0.83[CEU][hapmap]
rs316405	0.82[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs316408	0.83[CEU][hapmap]
rs316409	0.82[ASN][1000 genomes]
rs316410	0.82[ASN][1000 genomes]
rs316411	0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs316413	0.83[CEU][hapmap]
rs316418	0.82[ASN][1000 genomes]
rs3207358	0.82[ASN][1000 genomes]
rs34808919	0.82[ASN][1000 genomes]
rs35085573	0.85[ASN][1000 genomes]
rs35541316	0.82[ASN][1000 genomes]
rs35953019	0.81[JPT][hapmap]
rs36039989	0.80[ASN][1000 genomes]
rs3733839	0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4498259	0.81[JPT][hapmap]
rs493097	0.82[ASN][1000 genomes]
rs504404	0.80[ASN][1000 genomes]
rs541143	0.80[JPT][hapmap]
rs581914	0.85[ASN][1000 genomes]
rs62367685	0.82[ASN][1000 genomes]
rs62367688	0.84[ASN][1000 genomes]
rs6414900	0.81[JPT][hapmap]
rs6451674	0.81[JPT][hapmap]
rs6451675	0.81[JPT][hapmap]
rs670206	0.82[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs6862639	0.81[JPT][hapmap]
rs6864223	0.80[ASN][1000 genomes]
rs6871636	0.81[JPT][hapmap]
rs6884303	0.81[JPT][hapmap]
rs6894506	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs7709181	0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs7729529	0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs7730004	0.81[JPT][hapmap]

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	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
8	nsv968169	chr5:42956713-43043472	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	116 gene(s)	inside rSNPs	diseases
9	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
10	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43020800-43038400	Weak transcription	Spleen	Spleen
2	chr5:43021200-43038600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:43035000-43038600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:43035200-43039600	Weak transcription	Hela-S3	cervix
5	chr5:43035600-43039200	Weak transcription	HepG2	liver
6	chr5:43035800-43039400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:43036800-43038200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr5:43036800-43039000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr5:43036800-43039600	Active TSS	Placenta	Placenta
10	chr5:43036800-43043800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:43037000-43038200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr5:43037000-43038200	Active TSS	Adipose Nuclei	Adipose
13	chr5:43037000-43038200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
14	chr5:43037000-43038400	Active TSS	NHDF-Ad	bronchial
15	chr5:43037000-43039000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr5:43037000-43039000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr5:43037000-43039000	Flanking Active TSS	NHEK	skin
18	chr5:43037000-43039600	Bivalent/Poised TSS	Left Ventricle	heart
19	chr5:43037000-43040200	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr5:43037000-43040400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:43037000-43042200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
22	chr5:43037200-43038600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:43037200-43038600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
24	chr5:43037200-43038600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
25	chr5:43037200-43038800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr5:43037200-43039000	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr5:43037200-43039600	Active TSS	Muscle Satellite Cultured Cells	--
28	chr5:43037200-43040000	Active TSS	Lung	lung
29	chr5:43037200-43042400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
30	chr5:43037200-43042800	Active TSS	Right Ventricle	heart
31	chr5:43037400-43038200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
32	chr5:43037400-43038200	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr5:43037400-43038400	Active TSS	Pancreas	Pancrea
34	chr5:43037400-43038600	Bivalent/Poised TSS	Brain Substantia Nigra	brain
35	chr5:43037400-43038600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
36	chr5:43037400-43038600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
37	chr5:43037400-43038600	Active TSS	HSMMtube	muscle
38	chr5:43037400-43038800	Flanking Bivalent TSS/Enh	Liver	Liver
39	chr5:43037400-43038800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:43037400-43039000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr5:43037400-43039400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:43037400-43039600	Active TSS	Esophagus	oesophagus
43	chr5:43037400-43040000	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr5:43037400-43043000	Active TSS	HSMM	muscle
45	chr5:43037400-43045000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:43037600-43038200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:43037600-43038400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:43037600-43038600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr5:43037600-43038600	Flanking Bivalent TSS/Enh	Fetal Lung	lung
50	chr5:43037600-43038600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle

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