Variant report

Variant	rs13314464
Chromosome Location	chr3:119041408-119041409
allele	C/G
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	POLR2A	chr3:119041258-119042260	A549	lung:	n/a	n/a
2	POLR2A	chr3:119041212-119042480	GM18951	blood:	n/a	n/a
3	HDAC2	chr3:119041299-119041988	H1-hESC	embryonic stem cell:	n/a	n/a
4	SP1	chr3:119041198-119042184	A549	lung:	n/a	chr3:119041681-119041693 chr3:119041678-119041692 chr3:119041684-119041698 chr3:119041795-119041807 chr3:119041293-119041307 chr3:119041682-119041691 chr3:119041797-119041806 chr3:119041419-119041429 chr3:119041795-119041807 chr3:119041796-119041805
5	POLR2A	chr3:119040718-119042639	IMR90	lung:	n/a	n/a
6	MYC	chr3:119041317-119042420	NB4	blood:	n/a	chr3:119042031-119042041
7	REST	chr3:119041382-119041595	A549	lung:	n/a	chr3:119041382-119041395
8	MAZ	chr3:119041256-119042179	K562	blood:	n/a	chr3:119042031-119042041
9	ZNF263	chr3:119041262-119042548	HEK293-T-REx	kidney:	n/a	chr3:119041626-119041635
10	MAX	chr3:119041247-119041564	K562	blood:	n/a	n/a
11	CTCF	chr3:119041380-119041610	HCT-116	colon:	n/a	n/a
12	ZBTB7A	chr3:119041279-119042418	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr3:119041260-119042608	GM18526	blood:	n/a	n/a
14	RELA	chr3:119040978-119042718	GM15510	blood:	n/a	chr3:119042019-119042028 chr3:119042019-119042028
15	POLR2A	chr3:119041191-119042416	PANC-1	pancreas:	n/a	n/a
16	ELF1	chr3:119041161-119042626	GM12878	blood:	n/a	n/a
17	EGR1	chr3:119041254-119042161	H1-hESC	embryonic stem cell:	n/a	chr3:119041397-119041407 chr3:119041792-119041805 chr3:119041416-119041430 chr3:119041397-119041408 chr3:119041393-119041407 chr3:119041397-119041407 chr3:119041396-119041409 chr3:119042088-119042098 chr3:119041396-119041409 chr3:119041396-119041409 chr3:119041397-119041406 chr3:119041395-119041409
18	POLR2A	chr3:119041313-119042281	Gliobla	brain:	n/a	n/a
19	POLR2A	chr3:119041160-119042349	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:119041349-119042635	MCF-7	breast:	n/a	n/a
21	POLR2A	chr3:119040800-119042455	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:119041099-119042674	GM12892	blood:	n/a	n/a
23	POLR2A	chr3:119041228-119042384	MCF-7	breast:	n/a	n/a
24	POLR2A	chr3:119041010-119042487	GM12878	blood:	n/a	n/a
25	TCF12	chr3:119041380-119042426	A549	lung:	n/a	chr3:119041646-119041656
26	POLR2A	chr3:119041252-119042259	A549	lung:	n/a	n/a
27	POLR2A	chr3:119041124-119042804	GM12891	blood:	n/a	n/a
28	POLR2A	chr3:119041112-119042314	HUVEC	blood vessel:	n/a	n/a
29	EBF1	chr3:119041209-119041533	GM12878	blood:	n/a	n/a
30	CTCF	chr3:119041353-119042029	GM12891	blood:	n/a	chr3:119041959-119041972 chr3:119041729-119041750 chr3:119041736-119041749 chr3:119041676-119041689 chr3:119041734-119041752 chr3:119041676-119041685
31	POU2F2	chr3:119041194-119042536	GM12891	blood:	n/a	n/a
32	POLR2A	chr3:119041061-119042721	GM18505	blood:	n/a	n/a
33	RAD21	chr3:119041343-119042305	H1-hESC	embryonic stem cell:	n/a	chr3:119041734-119041746 chr3:119042155-119042165 chr3:119041732-119041751 chr3:119041735-119041748
34	MXI1	chr3:119041340-119042055	H1-hESC	embryonic stem cell:	n/a	n/a
35	MTA3	chr3:119040824-119043149	GM12878	blood:	n/a	n/a
36	MAX	chr3:119041145-119042476	HCT-116	colon:	n/a	chr3:119042031-119042041
37	REST	chr3:119041115-119042498	H1-neurons	neurons:	n/a	chr3:119042184-119042194 chr3:119041382-119041395 chr3:119042182-119042196
38	POLR2A	chr3:119041035-119042495	GM12891	blood:	n/a	n/a
39	SIN3A	chr3:119041183-119042631	H1-hESC	embryonic stem cell:	n/a	chr3:119041382-119041395 chr3:119042179-119042190 chr3:119042183-119042197
40	POLR2A	chr3:119041322-119042378	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr3:119041121-119041565	HUVEC	blood vessel:	n/a	n/a
42	ZMIZ1	chr3:119041405-119041433	K562	blood:	n/a	n/a
43	MAZ	chr3:119040868-119042539	IMR90	lung:	n/a	chr3:119042031-119042041
44	POLR2A	chr3:119041047-119042615	GM12891	blood:	n/a	n/a
45	MAX	chr3:119041149-119042362	A549	lung:	n/a	chr3:119042031-119042041
46	CREB1	chr3:119041158-119042651	GM12878	blood:	n/a	n/a
47	TAF1	chr3:119041354-119042337	H1-hESC	embryonic stem cell:	n/a	n/a
48	CHD1	chr3:119041227-119042428	GM12878	blood:	n/a	n/a
49	EGR1	chr3:119041272-119041610	K562	blood:	n/a	chr3:119041397-119041407 chr3:119041416-119041430 chr3:119041397-119041408 chr3:119041393-119041407 chr3:119041397-119041407 chr3:119041396-119041409 chr3:119041396-119041409 chr3:119041396-119041409 chr3:119041397-119041406 chr3:119041395-119041409
50	SMARCB1	chr3:119041367-119042619	Hela-S3	cervix:	n/a	chr3:119042066-119042075

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:119041383-119041433	T-47D	breast:	n/a
2	chr3:119041385-119041435	H1-hESC	embryonic stem cell:	embryo
3	chr3:119041383-119041433	NH-A	brain:	n/a
4	chr3:119041385-119041435	SK-N-MC	brain:	n/a
5	chr3:119041385-119041435	NHDF-neo	bronchial:	n/a
6	chr3:119041385-119041435	SK-N-SH	brain:	n/a
7	chr3:119041385-119041435	AG09319	gingival:	n/a
8	chr3:119041383-119041433	SAEC	small airway:	n/a
9	chr3:119041383-119041433	ProgFib	skin:	n/a
10	chr3:119041385-119041435	NB4	blood:	n/a
11	chr3:119041385-119041435	GM12878	blood:	n/a
12	chr3:119041383-119041433	HIPEpiC	eye:	n/a
13	chr3:119041385-119041435	HepG2	liver:	n/a
14	chr3:119041383-119041433	Hepatocyte	liver:	n/a
15	chr3:119041385-119041435	RPTEC	kidney:	n/a
16	chr3:119041385-119041435	HCM	heart:	n/a
17	chr3:119041383-119041433	HNPCEpiC	eye:	n/a
18	chr3:119041385-119041435	HCF	heart:	n/a
19	chr3:119041385-119041435	PANC-1	pancreas:	n/a
20	chr3:119041385-119041435	A549	lung:	n/a
21	chr3:119041383-119041433	HPAEpiC	pulmonary alveolar:	n/a
22	chr3:119041383-119041433	H1-hESC	embryonic stem cell:	embryo
23	chr3:119041385-119041435	SAEC	small airway:	n/a
24	chr3:119041385-119041435	HAEpiC	amniotic membrane:	n/a
25	chr3:119041385-119041435	HUVEC	blood vessel:	n/a
26	chr3:119041385-119041435	HRE	kidney:	n/a
27	chr3:119041385-119041435	GM12892	blood:	n/a
28	chr3:119041383-119041433	NHBE	bronchial:	n/a
29	chr3:119041383-119041433	HCF	heart:	n/a
30	chr3:119041385-119041435	NHBE	bronchial:	n/a
31	chr3:119041385-119041435	AoSMC	blood vessel:	n/a
32	chr3:119041383-119041433	SK-N-SH_RA	brain:	n/a
33	chr3:119041385-119041435	IMR90	lung:	fetal
34	chr3:119041385-119041435	HEK293	kidney:	embryo
35	chr3:119041383-119041433	U87	brain:	n/a
36	chr3:119041385-119041435	Jurkat	blood:	n/a
37	chr3:119041383-119041433	HEK293	kidney:	embryo
38	chr3:119041383-119041433	GM12892	blood:	n/a
39	chr3:119041385-119041435	GM06990	blood:	n/a
40	chr3:119041383-119041433	HRCEpiC	kidney:	n/a
41	chr3:119041385-119041435	HNPCEpiC	eye:	n/a
42	chr3:119041385-119041435	K562	blood:	n/a
43	chr3:119041383-119041433	ovcar-3	ovarian:	n/a
44	chr3:119041383-119041433	AoSMC	blood vessel:	n/a
45	chr3:119041383-119041433	IMR90	lung:	fetal
46	chr3:119041383-119041433	HMEC	breast:	n/a
47	chr3:119041383-119041433	GM19239	blood:	n/a
48	chr3:119041383-119041433	HCT-116	colon:	n/a
49	chr3:119041385-119041435	HMEC	breast:	n/a
50	chr3:119041385-119041435	ProgFib	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:119040381..119043387-chr3:119393976..119396207,3	K562	blood:
2	chr3:119039655..119042714-chr3:119058706..119061390,3	MCF-7	breast:
3	chr15:101817168..101817800-chr3:119041367..119041890,2	NB4	blood:
4	chr3:119016211..119028042-chr3:119037960..119043695,12	MCF-7	breast:
5	chr3:119012312..119014941-chr3:119040203..119043471,4	MCF-7	breast:
6	chr3:119011662..119015799-chr3:119040784..119043293,4	MCF-7	breast:
7	chr3:119040625..119043456-chr3:119181021..119182647,3	MCF-7	breast:
8	chr3:119040520..119043561-chr3:119060040..119062334,3	MCF-7	breast:

Variant related genes	Relation type
ARHGAP31	TF binding region
ARHGAP31	CpG island
ENSG00000131871	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000207310	Chromatin interaction
ENSG00000031081	Chromatin interaction
ENSG00000242829	Chromatin interaction
ENSG00000138495	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10511386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10934490	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375135	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1448434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2278781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4687994	0.84[EUR][1000 genomes]
rs58568360	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62265236	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62265237	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6438518	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6438519	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6438520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6438521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6438522	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6438523	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6762580	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6785727	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786522	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789881	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799733	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610546	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7611832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7619210	0.83[EUR][1000 genomes]
rs7644570	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7649480	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7649930	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822211	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825078	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9834750	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847963	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9861372	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861688	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877740	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119040600-119041600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr3:119040600-119041600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:119040600-119041600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:119040600-119041800	Flanking Active TSS	NH-A	brain
5	chr3:119040600-119042400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:119040600-119042400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr3:119040600-119042600	Flanking Active TSS	HUVEC	blood vessel
8	chr3:119040600-119043000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:119040600-119043000	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr3:119040800-119041600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:119040800-119041600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr3:119040800-119041600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr3:119040800-119041600	Flanking Active TSS	Fetal Muscle Leg	muscle
14	chr3:119040800-119041800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr3:119040800-119041800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:119040800-119042200	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr3:119040800-119042400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:119040800-119042400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:119040800-119042600	Flanking Active TSS	Dnd41	blood
20	chr3:119040800-119042800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr3:119041000-119041600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr3:119041000-119041600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:119041000-119041600	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr3:119041000-119041600	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr3:119041000-119041600	Flanking Active TSS	Esophagus	oesophagus
26	chr3:119041000-119041600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr3:119041000-119041600	Flanking Active TSS	Fetal Intestine Small	intestine
28	chr3:119041000-119041600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr3:119041000-119041600	Flanking Active TSS	Rectal Smooth Muscle	rectum
30	chr3:119041000-119041600	Flanking Active TSS	Right Atrium	heart
31	chr3:119041000-119041600	Flanking Active TSS	Thymus	Thymus
32	chr3:119041000-119041600	Flanking Active TSS	HSMM	muscle
33	chr3:119041000-119041600	Flanking Active TSS	HSMMtube	muscle
34	chr3:119041000-119041800	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr3:119041000-119041800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr3:119041000-119041800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:119041000-119041800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:119041000-119041800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:119041000-119041800	Flanking Active TSS	Fetal Muscle Trunk	muscle
40	chr3:119041000-119041800	Flanking Active TSS	Placenta	Placenta
41	chr3:119041000-119041800	Flanking Active TSS	Fetal Thymus	thymus
42	chr3:119041000-119041800	Active TSS	Right Ventricle	heart
43	chr3:119041000-119041800	Flanking Active TSS	HepG2	liver
44	chr3:119041000-119042200	Active TSS	Fetal Brain Female	brain
45	chr3:119041000-119042400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:119041000-119042400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:119041000-119042400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:119041000-119042400	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr3:119041000-119042400	Active TSS	Brain Germinal Matrix	brain
50	chr3:119041000-119042400	Active TSS	Brain Substantia Nigra	brain

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