Variant report

Variant	rs3574
Chromosome Location	chr16:30411382-30411383
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	MBD4	chr16:30410967-30411682	HepG2	liver:	n/a	n/a
2	BCL3	chr16:30411008-30412230	A549	lung:	n/a	chr16:30411839-30411852 chr16:30411760-30411769 chr16:30411566-30411579 chr16:30412109-30412122 chr16:30411761-30411770
3	POLR2A	chr16:30411003-30412307	K562	blood:	n/a	n/a
4	TAF1	chr16:30411283-30412276	H1-neurons	neurons:	n/a	n/a
5	SIN3AK20	chr16:30411222-30412384	MCF-7	breast:	n/a	n/a
6	ELF1	chr16:30411380-30412265	GM12878	blood:	n/a	n/a
7	MAX	chr16:30411363-30412381	HepG2	liver:	n/a	chr16:30411760-30411769 chr16:30411628-30411637 chr16:30411761-30411770
8	PML	chr16:30411303-30412347	MCF-7	breast:	n/a	n/a
9	RUNX3	chr16:30411137-30412254	GM12878	blood:	n/a	n/a
10	SIN3AK20	chr16:30411371-30412209	PFSK-1	brain:	n/a	n/a
11	MAX	chr16:30411182-30412354	A549	lung:	n/a	chr16:30411760-30411769 chr16:30411628-30411637 chr16:30411761-30411770
12	ZBTB33	chr16:30411089-30412331	A549	lung:	n/a	chr16:30412038-30412047 chr16:30412039-30412049 chr16:30412036-30412046 chr16:30412036-30412051
13	ELF1	chr16:30411351-30412414	GM12878	blood:	n/a	n/a
14	NFATC1	chr16:30411141-30412272	GM12878	blood:	n/a	n/a
15	KAP1	chr16:30411012-30412220	HEK293	kidney:	n/a	n/a
16	KAP1	chr16:30411011-30412251	U2OS	brain:	n/a	n/a
17	CTCF	chr16:30411260-30411410	HCPEpiC	choroid plexus:	n/a	n/a
18	POLR2A	chr16:30411009-30412226	Hela-S3	cervix:	n/a	n/a
19	CHD1	chr16:30411210-30412046	H1-hESC	embryonic stem cell:	n/a	n/a
20	MXI1	chr16:30410862-30412528	IMR90	lung:	n/a	chr16:30411626-30411641 chr16:30411628-30411643
21	MAX	chr16:30411152-30412324	ECC-1	luminal epithelium:	n/a	chr16:30411760-30411769 chr16:30411628-30411637 chr16:30411761-30411770
22	CEBPB	chr16:30411284-30411892	GM12878	blood:	n/a	n/a
23	JUND	chr16:30410902-30412234	SK-N-SH	brain:	n/a	chr16:30411762-30411769 chr16:30411760-30411770 chr16:30411759-30411770 chr16:30411761-30411770 chr16:30411761-30411769
24	RAD21	chr16:30411378-30411564	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr16:30410274-30412354	HepG2	liver:	n/a	n/a
26	POLR2A	chr16:30410692-30412367	PANC-1	pancreas:	n/a	n/a
27	TCF7L2	chr16:30411228-30412131	MCF-7	breast:	n/a	chr16:30411761-30411770
28	PBX3	chr16:30411018-30412147	A549	lung:	n/a	n/a
29	EGR1	chr16:30411323-30412349	HCT-116	colon:	n/a	chr16:30411524-30411535 chr16:30411987-30412000 chr16:30411602-30411617 chr16:30411603-30411616
30	POLR2A	chr16:30410086-30412282	H1-hESC	embryonic stem cell:	n/a	n/a
31	PBX3	chr16:30411355-30412274	A549	lung:	n/a	n/a
32	STAT5A	chr16:30411341-30412139	GM12878	blood:	n/a	chr16:30411760-30411769 chr16:30411761-30411770
33	FOXM1	chr16:30411214-30412328	GM12878	blood:	n/a	n/a
34	ZNF263	chr16:30411327-30412257	HEK293-T-REx	kidney:	n/a	chr16:30411594-30411603
35	POLR2A	chr16:30409690-30412303	SK-N-MC	brain:	n/a	n/a
36	POLR2A	chr16:30411012-30412402	HUVEC	blood vessel:	n/a	n/a
37	E2F6	chr16:30411326-30412392	A549	lung:	n/a	chr16:30411700-30411709 chr16:30412109-30412118 chr16:30411982-30411993 chr16:30411847-30411857 chr16:30411983-30411995
38	SRF	chr16:30411289-30411873	ECC-1	luminal epithelium:	n/a	chr16:30411550-30411563
39	GATA3	chr16:30411127-30412386	A549	lung:	n/a	chr16:30411762-30411771
40	POLR2A	chr16:30409772-30411750	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr16:30410514-30412326	H1-neurons	neurons:	n/a	n/a
42	ATF3	chr16:30411371-30411947	A549	lung:	n/a	n/a
43	POLR2A	chr16:30409890-30412277	H1-hESC	embryonic stem cell:	n/a	n/a
44	ZBTB7A	chr16:30411107-30412199	ECC-1	luminal epithelium:	n/a	n/a
45	EGR1	chr16:30411382-30411805	ECC-1	luminal epithelium:	n/a	chr16:30411524-30411535 chr16:30411602-30411617 chr16:30411603-30411616
46	POLR2A	chr16:30410676-30411406	GM12892	blood:	n/a	n/a
47	REST	chr16:30410856-30412310	H1-neurons	neurons:	n/a	n/a
48	TBP	chr16:30411370-30412259	H1-hESC	embryonic stem cell:	n/a	n/a
49	SIN3AK20	chr16:30410945-30412271	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr16:30411373-30412406	Hela-S3	cervix:	n/a	n/a

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	chr16:30364406..30367018-chr16:30410675..30414452,3	MCF-7	breast:
4	chr16:30386182..30395144-chr16:30402818..30414477,44	MCF-7	breast:
5	chr16:30385968..30392864-chr16:30403786..30414800,30	MCF-7	breast:
6	chr16:30391099..30394123-chr16:30410242..30411998,4	K562	blood:
7	chr16:30387676..30396507-chr16:30404234..30411930,28	K562	blood:
8	chr16:30409685..30411785-chr16:30564140..30566848,3	MCF-7	breast:
9	chr16:30409830..30411991-chr16:30671268..30673379,2	MCF-7	breast:
10	chr16:30409223..30411456-chr16:30453494..30456460,2	MCF-7	breast:
11	chr16:30380346..30383247-chr16:30410530..30413026,3	K562	blood:
12	chr16:30378819..30383918-chr16:30407597..30413128,8	MCF-7	breast:
13	chr16:30368801..30385970-chr16:30403825..30413311,30	MCF-7	breast:
14	chr16:30388826..30390793-chr16:30410423..30412257,2	K562	blood:
15	chr16:30061476..30064810-chr16:30408529..30411930,3	MCF-7	breast:
16	chr16:30408965..30411877-chr16:30643615..30646400,2	MCF-7	breast:
17	chr16:30366670..30368244-chr16:30410921..30413124,2	K562	blood:

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

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11150586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11646130	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11862806	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11863150	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs12446288	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12447833	0.92[ASN][1000 genomes]
rs12921440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13333093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35480350	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35598865	1.00[JPT][hapmap]
rs4340343	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4465620	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4787642	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4787643	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4788409	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4788413	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788414	0.82[EUR][1000 genomes]
rs62055459	0.90[ASN][1000 genomes]
rs6565182	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6565183	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7203359	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8046445	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8049108	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8050812	1.00[JPT][hapmap]
rs8051096	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8060853	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9888967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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
rs3574	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL
rs3574	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30407600-30411400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr16:30408200-30411400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr16:30409400-30411400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr16:30409800-30411600	Enhancers	Stomach Mucosa	stomach
5	chr16:30410000-30411400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr16:30410200-30411400	Weak transcription	Esophagus	oesophagus
7	chr16:30410400-30411400	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr16:30410400-30411400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr16:30410600-30411400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr16:30410600-30411400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr16:30410600-30411400	Enhancers	Spleen	Spleen
12	chr16:30410600-30412200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr16:30410600-30412400	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr16:30410800-30411400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr16:30410800-30411400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr16:30410800-30411400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr16:30410800-30411400	Enhancers	Placenta	Placenta
18	chr16:30410800-30411400	Enhancers	Pancreas	Pancrea
19	chr16:30410800-30411600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr16:30410800-30411600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr16:30410800-30411600	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr16:30410800-30411800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr16:30410800-30411800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr16:30410800-30412400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr16:30410800-30412400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr16:30410800-30412600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr16:30411000-30411400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr16:30411000-30411400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
29	chr16:30411000-30411400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr16:30411000-30411400	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr16:30411000-30411400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr16:30411000-30411400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr16:30411000-30411400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr16:30411000-30411400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr16:30411000-30411400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr16:30411000-30411400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
37	chr16:30411000-30411400	Enhancers	Primary B cells from peripheral blood	blood
38	chr16:30411000-30411400	Enhancers	Brain Angular Gyrus	brain
39	chr16:30411000-30411400	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr16:30411000-30411400	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr16:30411000-30411400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr16:30411000-30411400	Flanking Active TSS	Fetal Heart	heart
43	chr16:30411000-30411400	Flanking Active TSS	Fetal Lung	lung
44	chr16:30411000-30411400	Enhancers	Gastric	stomach
45	chr16:30411000-30411400	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr16:30411000-30411400	Flanking Active TSS	HSMM	muscle
47	chr16:30411000-30411600	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr16:30411000-30411600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr16:30411000-30411600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr16:30411000-30411600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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