Variant report

Variant	rs11862806
Chromosome Location	chr16:30364071-30364072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr16:30363960-30364110	HAc	cerebellar:	n/a	n/a
2	CEBPD	chr16:30363807-30364181	HepG2	liver:	n/a	n/a
3	MBD4	chr16:30363289-30364855	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:30362407-30364951	HepG2	liver:	n/a	n/a
5	FOSL2	chr16:30362903-30364923	HepG2	liver:	n/a	n/a
6	CTCF	chr16:30364000-30364150	GM12873	blood:	n/a	n/a
7	POLR2A	chr16:30363894-30364875	HepG2	liver:	n/a	n/a
8	POLR2A	chr16:30363228-30364132	K562	blood:	n/a	n/a
9	POLR2A	chr16:30360110-30369693	HepG2	liver:	n/a	n/a
10	POLR2A	chr16:30363269-30365340	HepG2	liver:	n/a	n/a
11	POLR2A	chr16:30363901-30365011	HepG2	liver:	n/a	n/a
12	POLR2A	chr16:30362863-30364114	K562	blood:	n/a	n/a
13	POLR2A	chr16:30361391-30369063	HepG2	liver:	n/a	n/a
14	POLR2A	chr16:30362848-30364698	HepG2	liver:	n/a	n/a
15	POLR2A	chr16:30363989-30364141	HepG2	liver:	n/a	n/a
16	CTCF	chr16:30364020-30364170	GM12872	blood:	n/a	n/a
17	MYBL2	chr16:30363946-30364915	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30352836..30354996-chr16:30361711..30364215,3	MCF-7	breast:
2	chr16:30362931..30364603-chr16:30670116..30672156,2	MCF-7	breast:
3	chr16:30352018..30354581-chr16:30361515..30364164,2	K562	blood:
4	chr16:30363920..30364479-chr16:30420652..30421386,2	MCF-7	breast:
5	chr16:30347434..30350400-chr16:30361325..30364299,2	K562	blood:
6	chr16:30364024..30368341-chr16:30387690..30394486,12	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260219	TF binding region
ENSG00000180209	Chromatin interaction
ENSG00000180035	Chromatin interaction
ENSG00000270466	Chromatin interaction
ENSG00000180096	Chromatin interaction
ENSG00000156860	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11150586	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs11642676	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11644392	0.88[ASN][1000 genomes]
rs11645581	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11646130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11863150	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12446288	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12447833	0.88[EUR][1000 genomes]
rs12921440	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs12922786	0.91[ASN][1000 genomes]
rs12930787	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13333093	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs2911213	0.89[ASN][1000 genomes]
rs35480350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35598865	1.00[JPT][hapmap]
rs3574	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4465620	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs4471699	0.90[ASN][1000 genomes]
rs4787642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4787643	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs4788408	0.91[ASN][1000 genomes]
rs4788409	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs4788413	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62055459	0.85[EUR][1000 genomes]
rs6565178	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6565180	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6565182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6565183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68051857	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7186541	0.88[ASN][1000 genomes]
rs7195216	0.88[ASN][1000 genomes]
rs7203359	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs73532600	0.83[EUR][1000 genomes]
rs7404371	0.91[ASN][1000 genomes]
rs8046445	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8049108	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8050176	0.91[ASN][1000 genomes]
rs8050812	1.00[JPT][hapmap]
rs8051096	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8060853	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs9921711	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv2758420	chr16:30073955-30383280	Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
4	esv2758642	chr16:30073955-30383280	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11862806	TBX6	cis	parietal	SCAN
rs11862806	MAPK3	cis	parietal	SCAN
rs11862806	SEPHS2	cis	cerebellum	SCAN
rs11862806	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL
rs11862806	GDPD3	cis	cerebellum	SCAN
rs11862806	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30360200-30365600	Weak transcription	Fetal Kidney	kidney
2	chr16:30360400-30365000	Strong transcription	Primary T helper cells PMA-I stimulated	--
3	chr16:30360600-30364600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr16:30360600-30365200	Strong transcription	Sigmoid Colon	Sigmoid Colon
5	chr16:30360600-30365200	Strong transcription	NHEK	skin
6	chr16:30360800-30365000	Strong transcription	Fetal Thymus	thymus
7	chr16:30360800-30365200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:30361000-30364400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr16:30361000-30364400	Strong transcription	Placenta	Placenta
10	chr16:30361000-30364600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr16:30361000-30364600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr16:30361000-30364600	Strong transcription	K562	blood
13	chr16:30361000-30365200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr16:30361000-30365200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr16:30361000-30365200	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr16:30361000-30365400	Strong transcription	Primary T cells from cord blood	blood
17	chr16:30361000-30365400	Genic enhancers	Fetal Intestine Small	intestine
18	chr16:30361000-30365400	Strong transcription	Thymus	Thymus
19	chr16:30361200-30364800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr16:30361200-30365000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr16:30361200-30365200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr16:30361200-30365400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr16:30361400-30364400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr16:30361400-30365200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr16:30361400-30365200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr16:30361600-30364800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr16:30361600-30364800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
28	chr16:30361600-30365000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr16:30361600-30365000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr16:30361600-30365000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr16:30361600-30365000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr16:30361600-30365200	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr16:30361600-30365200	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr16:30361600-30365400	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr16:30361600-30365400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr16:30361600-30365400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr16:30361600-30365400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr16:30361600-30365400	Genic enhancers	Duodenum Mucosa	Duodenum
39	chr16:30361600-30365600	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr16:30361600-30366000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr16:30361800-30364200	Genic enhancers	NH-A	brain
42	chr16:30361800-30364400	Genic enhancers	HUVEC	blood vessel
43	chr16:30361800-30364800	Genic enhancers	Liver	Liver
44	chr16:30361800-30365400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr16:30361800-30365400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr16:30362000-30364400	Strong transcription	Colonic Mucosa	Colon
47	chr16:30362000-30364600	Strong transcription	Primary hematopoietic stem cells	blood
48	chr16:30362000-30364800	Strong transcription	Primary B cells from cord blood	blood
49	chr16:30362000-30365000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr16:30362000-30365000	Strong transcription	Placenta Amnion	Placenta Amnion

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