Variant report

Variant	rs3819662
Chromosome Location	chr22:33965497-33965498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:33964224..33966733-chr22:33974082..33975978,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1547069	0.85[ASN][1000 genomes]
rs1972207	0.85[ASN][1000 genomes]
rs1972209	0.82[ASN][1000 genomes]
rs2010833	0.93[ASN][1000 genomes]
rs2267232	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2283911	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.84[ASN][1000 genomes]
rs2283912	0.84[ASN][1000 genomes]
rs2283913	0.83[ASN][1000 genomes]
rs2283914	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.85[ASN][1000 genomes]
rs2283915	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.86[ASN][1000 genomes]
rs2283916	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2413193	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs3986016	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.85[ASN][1000 genomes]
rs4821161	0.85[ASN][1000 genomes]
rs5749629	0.86[ASN][1000 genomes]
rs5754603	0.82[ASN][1000 genomes]
rs6518832	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs762056	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs762061	0.91[ASN][1000 genomes]
rs988875	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs989556	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1062127	chr22:33755479-34085278	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544683	chr22:33755479-34085278	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv531588	chr22:33776857-34150188	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv914983	chr22:33800119-34035034	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1060283	chr22:33809137-34043739	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv544684	chr22:33809137-34043739	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1055791	chr22:33822226-34159536	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1065417	chr22:33823850-34053325	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
11	nsv933309	chr22:33825232-34053000	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
12	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
13	nsv917167	chr22:33852676-34137036	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1062832	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv544686	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv914986	chr22:33863218-33967289	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv914987	chr22:33920421-34047427	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
19	nsv1063312	chr22:33963672-33983973	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv588933	chr22:33963790-33978458	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3819662	C22orf31	cis	cerebellum	SCAN
rs3819662	KLHDC10	trans	parietal	SCAN
rs3819662	KREMEN1	cis	cerebellum	SCAN
rs3819662	LARGE	cis	cerebellum	SCAN
rs3819662	PES1	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33917400-33966800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr22:33940800-33970600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr22:33946000-33974600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr22:33949600-33975400	Weak transcription	Ovary	ovary
5	chr22:33952400-33969400	Weak transcription	A549	lung
6	chr22:33958400-33967000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr22:33959200-33966800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr22:33959400-33974800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr22:33960000-33966000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr22:33960000-33993000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr22:33960400-33969200	Weak transcription	Fetal Intestine Large	intestine
12	chr22:33961000-33969200	Weak transcription	Fetal Intestine Small	intestine
13	chr22:33962600-33967400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr22:33963000-33965600	Weak transcription	Small Intestine	intestine
15	chr22:33963400-33966200	Enhancers	Fetal Kidney	kidney
16	chr22:33963600-33966400	Enhancers	Right Ventricle	heart
17	chr22:33963800-33966200	Enhancers	Fetal Heart	heart
18	chr22:33963800-33966600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr22:33964000-33965600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr22:33964000-33965800	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr22:33964000-33966200	Enhancers	Primary hematopoietic stem cells	blood
22	chr22:33964000-33966200	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr22:33964000-33966200	Enhancers	Left Ventricle	heart
24	chr22:33964000-33966200	Enhancers	HepG2	liver
25	chr22:33964000-33966400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr22:33964000-33966400	Enhancers	Spleen	Spleen
27	chr22:33964200-33965800	Enhancers	Adipose Nuclei	Adipose
28	chr22:33964200-33965800	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr22:33964200-33966000	Enhancers	Right Atrium	heart
30	chr22:33964600-33966200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr22:33964600-33966400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr22:33964800-33965600	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr22:33964800-33965600	Enhancers	Rectal Smooth Muscle	rectum
34	chr22:33964800-33965800	Enhancers	Brain Germinal Matrix	brain
35	chr22:33964800-33965800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr22:33964800-33966000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr22:33964800-33966200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr22:33964800-33966200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr22:33964800-33966200	Enhancers	Fetal Stomach	stomach
40	chr22:33964800-33966400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr22:33964800-33967000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr22:33965000-33965600	Enhancers	Brain Anterior Caudate	brain
43	chr22:33965000-33965600	Enhancers	Fetal Lung	lung
44	chr22:33965000-33965600	Weak transcription	Lung	lung
45	chr22:33965000-33965800	Enhancers	Stomach Mucosa	stomach
46	chr22:33965000-33966000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr22:33965000-33966200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr22:33965000-33966200	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr22:33965000-33966400	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr22:33965000-33966400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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