Variant report

Variant	rs11083568
Chromosome Location	chr19:41319116-41319117
allele	A/C
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	chr19:41318917-41319377	GM12878	blood:	n/a	n/a
2	NFIC	chr19:41319016-41319464	ECC-1	luminal epithelium:	n/a	n/a
3	NR3C1	chr19:41319091-41319405	A549	lung:	n/a	chr19:41319226-41319247 chr19:41319229-41319243 chr19:41319262-41319275 chr19:41319229-41319243
4	POLR2A	chr19:41318805-41319116	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr19:41319040-41319356	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:41319022-41319329	A549	lung:	n/a	n/a
7	NR3C1	chr19:41318969-41319434	A549	lung:	n/a	chr19:41319226-41319247 chr19:41319229-41319243 chr19:41319262-41319275 chr19:41319229-41319243
8	NR3C1	chr19:41318640-41319423	A549	lung:	n/a	chr19:41319226-41319247 chr19:41319229-41319243 chr19:41319262-41319275 chr19:41319229-41319243
9	NR3C1	chr19:41318621-41319426	A549	lung:	n/a	chr19:41319226-41319247 chr19:41319229-41319243 chr19:41319262-41319275 chr19:41319229-41319243
10	POLR2A	chr19:41318760-41319307	K562	blood:	n/a	n/a
11	POLR2A	chr19:41318656-41319149	MCF10A-Er-Src	breast:	n/a	n/a
12	NR3C1	chr19:41319092-41319381	ECC-1	luminal epithelium:	n/a	chr19:41319226-41319247 chr19:41319229-41319243 chr19:41319262-41319275 chr19:41319229-41319243
13	NR3C1	chr19:41319028-41319399	A549	lung:	n/a	chr19:41319226-41319247 chr19:41319229-41319243 chr19:41319262-41319275 chr19:41319229-41319243
14	NR3C1	chr19:41319098-41319381	ECC-1	luminal epithelium:	n/a	chr19:41319226-41319247 chr19:41319229-41319243 chr19:41319262-41319275 chr19:41319229-41319243
15	POLR2A	chr19:41318914-41319339	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr19:41319084-41319412	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:41318940-41319335	K562	blood:	n/a	n/a
18	POLR2A	chr19:41319011-41319281	H1-neurons	neurons:	n/a	n/a
19	POLR2A	chr19:41319073-41319332	GM12878	blood:	n/a	n/a
20	NFIC	chr19:41319055-41319555	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr19:41318925-41319425	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41312625..41314191-chr19:41317244..41319686,2	MCF-7	breast:
2	chr19:41307688..41310230-chr19:41318329..41321323,2	MCF-7	breast:
3	chr19:41304267..41305951-chr19:41317494..41319797,2	MCF-7	breast:

Variant related genes	Relation type
CYP2T2P	TF binding region
ENSG00000269858	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10403040	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10405596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10411008	0.82[ASN][1000 genomes]
rs10413760	0.82[ASN][1000 genomes]
rs10416308	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10423139	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11083567	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881124	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs17713068	0.85[JPT][hapmap]
rs2287691	0.85[JPT][hapmap]
rs28660501	0.84[ASN][1000 genomes]
rs3745213	0.85[JPT][hapmap]
rs8113056	0.86[AMR][1000 genomes];0.95[ASN][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	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv521459	chr19:41313202-41333284	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11083568	ZNF230	cis	cerebellum	SCAN
rs11083568	GPR77	cis	parietal	SCAN
rs11083568	STRN4	cis	cerebellum	SCAN
rs11083568	ZNF114	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41315000-41324400	Weak transcription	HepG2	liver
2	chr19:41315000-41332600	Weak transcription	Aorta	Aorta
3	chr19:41316000-41319400	Enhancers	Spleen	Spleen
4	chr19:41316000-41319800	Enhancers	Fetal Heart	heart
5	chr19:41316200-41324400	Weak transcription	Gastric	stomach
6	chr19:41316400-41325400	Weak transcription	Dnd41	blood
7	chr19:41317200-41319200	Enhancers	Lung	lung
8	chr19:41317200-41320800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr19:41317400-41319800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:41317400-41320200	Enhancers	Placenta	Placenta
11	chr19:41317400-41320400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr19:41317600-41320400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:41317600-41324000	Weak transcription	Hela-S3	cervix
14	chr19:41317600-41324400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:41317800-41319200	Enhancers	Adipose Nuclei	Adipose
16	chr19:41317800-41319400	Enhancers	Colonic Mucosa	Colon
17	chr19:41317800-41320000	Enhancers	Brain Substantia Nigra	brain
18	chr19:41317800-41324200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr19:41317800-41324400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:41317800-41324400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr19:41318000-41319200	Enhancers	Duodenum Mucosa	Duodenum
22	chr19:41318000-41319400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:41318000-41324400	Weak transcription	Pancreas	Pancrea
24	chr19:41318000-41324400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr19:41318000-41324400	Weak transcription	Right Atrium	heart
26	chr19:41318200-41319200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:41318200-41319200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr19:41318200-41319200	Enhancers	Brain Anterior Caudate	brain
29	chr19:41318200-41319400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:41318200-41319400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:41318200-41319800	Enhancers	Colon Smooth Muscle	Colon
32	chr19:41318200-41319800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr19:41318200-41319800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr19:41318200-41319800	Enhancers	Ovary	ovary
35	chr19:41318200-41320000	Enhancers	Fetal Kidney	kidney
36	chr19:41318200-41320000	Enhancers	Rectal Smooth Muscle	rectum
37	chr19:41318200-41320200	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr19:41318200-41320200	Weak transcription	A549	lung
39	chr19:41318200-41320400	Enhancers	Fetal Stomach	stomach
40	chr19:41318200-41323600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr19:41318200-41323800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:41318200-41324400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr19:41318400-41319200	Enhancers	Fetal Intestine Small	intestine
44	chr19:41318400-41319400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr19:41318400-41319400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:41318400-41319400	Enhancers	Stomach Smooth Muscle	stomach
47	chr19:41318400-41319600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr19:41318400-41319800	Enhancers	Fetal Lung	lung
49	chr19:41318400-41319800	Enhancers	Fetal Muscle Leg	muscle
50	chr19:41318400-41320000	Enhancers	Brain Hippocampus Middle	brain

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