Variant report

Variant	rs4788413
Chromosome Location	chr16:30410445-30410446
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:61)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:30409339-30410673	K562	blood:	n/a	n/a
2	CTCF	chr16:30410320-30410470	HEK293	kidney:	n/a	n/a
3	POLR2A	chr16:30410274-30412354	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:30410086-30412282	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr16:30409690-30412303	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr16:30409772-30411750	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr16:30409890-30412277	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr16:30409617-30413472	HepG2	liver:	n/a	n/a
9	POLR2A	chr16:30410257-30412295	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr16:30410221-30410503	HCT-116	colon:	n/a	n/a
11	POLR2A	chr16:30410334-30410449	A549	lung:	n/a	n/a
12	POLR2A	chr16:30410198-30410478	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr16:30410241-30410462	A549	lung:	n/a	n/a
14	POLR2A	chr16:30408779-30412460	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:30410429-30410479	BJ	skin:	n/a
2	chr16:30410429-30410479	NT2-D1	testis:	n/a
3	chr16:30410429-30410479	H1-hESC	embryonic stem cell:	embryo
4	chr16:30410429-30410479	BE2_C	brain:	n/a
5	chr16:30410429-30410479	AG09309	skin:	n/a
6	chr16:30410429-30410479	GM12892	blood:	n/a
7	chr16:30410429-30410479	AG04449	skin:	fetal
8	chr16:30410429-30410479	K562	blood:	n/a
9	chr16:30410429-30410479	HCT-116	colon:	n/a
10	chr16:30410429-30410479	T-47D	breast:	n/a
11	chr16:30410429-30410479	SK-N-SH	brain:	n/a
12	chr16:30410429-30410479	SK-N-MC	brain:	n/a
13	chr16:30410429-30410479	PrEC	prostate:	n/a
14	chr16:30410429-30410479	NH-A	brain:	n/a
15	chr16:30410429-30410479	Caco-2	colon:	n/a
16	chr16:30410429-30410479	ECC-1	luminal epithelium:	n/a
17	chr16:30410429-30410479	AG04450	lung:	fetal
18	chr16:30410429-30410479	NB4	blood:	n/a
19	chr16:30410429-30410479	AG10803	skin:	n/a
20	chr16:30410429-30410479	SKMC	muscle:	n/a
21	chr16:30410429-30410479	ovcar-3	ovarian:	n/a
22	chr16:30410429-30410479	SAEC	small airway:	n/a
23	chr16:30410429-30410479	GM12878	blood:	n/a
24	chr16:30410429-30410479	SK-N-SH_RA	brain:	n/a
25	chr16:30410429-30410479	Jurkat	blood:	n/a
26	chr16:30410429-30410479	GM06990	blood:	n/a
27	chr16:30410429-30410479	PANC-1	pancreas:	n/a
28	chr16:30410429-30410479	HRE	kidney:	n/a
29	chr16:30410429-30410479	HPAEpiC	pulmonary alveolar:	n/a
30	chr16:30410429-30410479	HEEpiC	esophagus:	n/a
31	chr16:30410429-30410479	IMR90	lung:	fetal
32	chr16:30410429-30410479	U87	brain:	n/a
33	chr16:30410429-30410479	ProgFib	skin:	n/a
34	chr16:30410429-30410479	PFSK-1	brain:	n/a
35	chr16:30410429-30410479	HAEpiC	amniotic membrane:	n/a
36	chr16:30410429-30410479	HepG2	liver:	n/a
37	chr16:30410429-30410479	A549	lung:	n/a
38	chr16:30410429-30410479	HRCEpiC	kidney:	n/a
39	chr16:30410429-30410479	NHBE	bronchial:	n/a
40	chr16:30410429-30410479	HNPCEpiC	eye:	n/a
41	chr16:30410429-30410479	HCF	heart:	n/a
42	chr16:30410429-30410479	AG09319	gingival:	n/a
43	chr16:30410429-30410479	HL-60	blood:	n/a
44	chr16:30410429-30410479	HRPEpiC	eye:	n/a
45	chr16:30410429-30410479	HIPEpiC	eye:	n/a
46	chr16:30410429-30410479	GM19239	blood:	n/a
47	chr16:30410429-30410479	Hela-S3	cervix:	n/a
48	chr16:30410429-30410479	HMEC	breast:	n/a
49	chr16:30410429-30410479	HCM	heart:	n/a
50	chr16:30410429-30410479	CMK	blood:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr16:30409273..30413539-chr16:30663133..30666228,3	MCF-7	breast:
2	chr16:30365556..30368170-chr16:30409648..30412813,3	K562	blood:
3	chr16:30386182..30395144-chr16:30402818..30414477,44	MCF-7	breast:
4	chr16:30385968..30392864-chr16:30403786..30414800,30	MCF-7	breast:
5	chr16:30391099..30394123-chr16:30410242..30411998,4	K562	blood:
6	chr16:30387676..30396507-chr16:30404234..30411930,28	K562	blood:
7	chr16:30409685..30411785-chr16:30564140..30566848,3	MCF-7	breast:
8	chr16:30409830..30411991-chr16:30671268..30673379,2	MCF-7	breast:
9	chr16:30401749..30403997-chr16:30408377..30410909,4	K562	blood:
10	chr16:30409223..30411456-chr16:30453494..30456460,2	MCF-7	breast:
11	chr16:30378819..30383918-chr16:30407597..30413128,8	MCF-7	breast:
12	chr16:30368801..30385970-chr16:30403825..30413311,30	MCF-7	breast:
13	chr16:30388826..30390793-chr16:30410423..30412257,2	K562	blood:
14	chr16:30061476..30064810-chr16:30408529..30411930,3	MCF-7	breast:
15	chr16:30408965..30411877-chr16:30643615..30646400,2	MCF-7	breast:

No data

Variant related genes	Relation type
SEPT1	TF binding region
SEPT1	CpG island
ENSG00000180096	Chromatin interaction
ENSG00000169217	Chromatin interaction
ENSG00000180209	Chromatin interaction
ENSG00000156860	Chromatin interaction
ENSG00000149925	Chromatin interaction
ENSG00000169221	Chromatin interaction
ENSG00000260219	Chromatin interaction
ENSG00000149926	Chromatin interaction
ENSG00000180035	Chromatin interaction
ENSG00000156858	Chromatin interaction
ENSG00000270466	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11150586	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11640950	0.91[AFR][1000 genomes]
rs11642676	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11645581	0.81[EUR][1000 genomes]
rs11646130	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11862806	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11863150	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12165013	0.80[EUR][1000 genomes]
rs12446288	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12447833	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12921440	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13333093	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35480350	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35598865	1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs3574	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4340343	0.83[EUR][1000 genomes]
rs4465620	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4787642	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4787643	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4788409	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4788414	0.92[EUR][1000 genomes]
rs62055459	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6565182	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6565183	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7203359	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73532600	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8045252	0.91[AFR][1000 genomes]
rs8045570	0.91[AFR][1000 genomes]
rs8046445	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8049108	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs8050812	1.00[JPT][hapmap]
rs8051096	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8060853	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9888967	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9921711	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv1056897	chr16:30363683-30457504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv905724	chr16:30368591-30438930	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
6	nsv827612	chr16:30371538-30429862	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
7	nsv905725	chr16:30376959-30420851	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
8	nsv962197	chr16:30390489-30425618	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4788413	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL
rs4788413	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30407600-30411000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:30407600-30411400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr16:30407800-30410800	Weak transcription	HSMM	muscle
4	chr16:30407800-30410800	Weak transcription	NHDF-Ad	bronchial
5	chr16:30407800-30411000	Weak transcription	Fetal Kidney	kidney
6	chr16:30407800-30411200	Weak transcription	Psoas Muscle	Psoas
7	chr16:30408000-30410600	Weak transcription	NH-A	brain
8	chr16:30408000-30410800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr16:30408000-30410800	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr16:30408000-30411000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:30408000-30411000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr16:30408000-30411000	Weak transcription	Brain Angular Gyrus	brain
13	chr16:30408000-30411000	Weak transcription	Brain Substantia Nigra	brain
14	chr16:30408000-30411000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr16:30408000-30411000	Weak transcription	Fetal Lung	lung
16	chr16:30408000-30411000	Weak transcription	Right Atrium	heart
17	chr16:30408000-30411000	Weak transcription	GM12878-XiMat	blood
18	chr16:30408000-30411200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr16:30408000-30411200	Weak transcription	HMEC	breast
20	chr16:30408200-30410800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr16:30408200-30411000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr16:30408200-30411200	Weak transcription	Small Intestine	intestine
23	chr16:30408200-30411400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr16:30408400-30410600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr16:30408400-30410600	Strong transcription	Fetal Muscle Leg	muscle
26	chr16:30408400-30410800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr16:30408400-30410800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
28	chr16:30408400-30411000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr16:30408400-30411200	Weak transcription	Primary B cells from cord blood	blood
30	chr16:30408600-30410600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr16:30408600-30410600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr16:30408800-30410600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr16:30408800-30410600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr16:30408800-30410600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr16:30408800-30410600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr16:30408800-30410600	Strong transcription	Fetal Intestine Small	intestine
37	chr16:30408800-30410600	Genic enhancers	Stomach Smooth Muscle	stomach
38	chr16:30409000-30410600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr16:30409000-30410600	Weak transcription	K562	blood
40	chr16:30409000-30410800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr16:30409000-30410800	Strong transcription	NHLF	lung
42	chr16:30409000-30411000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr16:30409000-30411000	Weak transcription	Liver	Liver
44	chr16:30409000-30411200	Weak transcription	NHEK	skin
45	chr16:30409200-30410800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr16:30409200-30411000	Weak transcription	Hela-S3	cervix
47	chr16:30409200-30411200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr16:30409400-30410600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr16:30409400-30410800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr16:30409400-30411000	Enhancers	Fetal Brain Male	brain

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