Variant report

Variant	rs11097023
Chromosome Location	chr4:85505474-85505475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:85503339..85505737-chr4:85885750..85887907,3	MCF-7	breast:
2	chr4:85504642..85507062-chr4:85579993..85581642,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180769	Chromatin interaction
ENSG00000163625	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1020278	0.84[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs10446695	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs10776519	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11099651	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11099652	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11099653	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11725539	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11733870	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11929910	0.84[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12509774	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12648523	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13102661	0.94[GIH][hapmap];0.87[MEX][hapmap]
rs1372971	0.91[GIH][hapmap];0.87[MEX][hapmap]
rs1443074	0.94[GIH][hapmap]
rs2868914	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2868915	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2868916	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2868917	0.81[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2868919	0.84[CEU][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs2868920	0.82[CHD][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap]
rs35227341	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35909314	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4449405	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4533768	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6535544	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6829806	0.91[GIH][hapmap];0.87[MEX][hapmap]
rs7657036	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7657224	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7659340	0.84[CEU][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes]
rs7677285	0.88[CEU][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7678115	0.87[EUR][1000 genomes]
rs7678268	0.81[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9784491	0.91[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3427170	chr4:85503153-85505701	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11097023	NCRNA00247	cis	cerebellum	SCAN
rs11097023	NKX6-1	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85503200-85505600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr4:85503400-85505600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:85503400-85505800	Active TSS	Brain Angular Gyrus	brain
4	chr4:85503400-85505800	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr4:85503600-85505600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:85503600-85505600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:85503600-85505600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:85503600-85505600	Active TSS	Brain Cingulate Gyrus	brain
9	chr4:85503600-85505600	Active TSS	Brain Hippocampus Middle	brain
10	chr4:85503600-85505600	Bivalent/Poised TSS	Fetal Kidney	kidney
11	chr4:85503600-85505800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:85503600-85505800	Active TSS	Esophagus	oesophagus
13	chr4:85503600-85505800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
14	chr4:85503600-85506000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr4:85503600-85506200	Active TSS	Brain Anterior Caudate	brain
16	chr4:85503800-85505600	Active TSS	HMEC	breast
17	chr4:85503800-85505800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:85503800-85505800	Active TSS	Rectal Smooth Muscle	rectum
19	chr4:85503800-85505800	Active TSS	Right Ventricle	heart
20	chr4:85503800-85506600	Active TSS	H1 Cell Line	embryonic stem cell
21	chr4:85503800-85507000	Active TSS	Duodenum Mucosa	Duodenum
22	chr4:85503800-85507200	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr4:85504200-85505600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
24	chr4:85504400-85507000	Active TSS	Stomach Mucosa	stomach
25	chr4:85504600-85505800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
26	chr4:85504800-85505600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr4:85504800-85505600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
28	chr4:85504800-85505600	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
29	chr4:85504800-85505600	Bivalent/Poised TSS	Thymus	Thymus
30	chr4:85505000-85505600	ZNF genes & repeats	Fetal Heart	heart
31	chr4:85505000-85505800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:85505000-85505800	Active TSS	Colonic Mucosa	Colon
33	chr4:85505000-85505800	Bivalent/Poised TSS	Small Intestine	intestine
34	chr4:85505000-85506000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
35	chr4:85505000-85506400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
36	chr4:85505000-85506400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
37	chr4:85505000-85507400	Enhancers	Liver	Liver
38	chr4:85505200-85505600	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:85505200-85505600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
40	chr4:85505200-85505600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:85505200-85505600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
42	chr4:85505200-85505600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
43	chr4:85505200-85505600	Active TSS	Placenta	Placenta
44	chr4:85505200-85505600	Active TSS	Stomach Smooth Muscle	stomach
45	chr4:85505200-85505800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:85505200-85505800	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr4:85505200-85506000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:85505200-85506000	Active TSS	Fetal Stomach	stomach
49	chr4:85505200-85506200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
50	chr4:85505200-85506400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell

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