Variant report

Variant	rs5763315
Chromosome Location	chr22:29939683-29939684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29938856..29940364-chr22:29948151..29949773,2	MCF-7	breast:
2	chr22:29938209..29940408-chr22:29946980..29949798,2	K562	blood:
3	chr22:29938437..29940751-chr22:29944125..29946145,2	K562	blood:
4	chr22:29935399..29937361-chr22:29938539..29940418,2	K562	blood:

Variant related genes	Relation type
ENSG00000100296	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1009147	0.80[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs105268	1.00[JPT][hapmap]
rs11090576	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs165602	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs165607	1.00[JPT][hapmap];0.83[TSI][hapmap]
rs165624	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs165633	1.00[JPT][hapmap]
rs165649	1.00[JPT][hapmap]
rs165734	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs165821	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs165853	0.92[ASN][1000 genomes]
rs165899	0.81[ASN][1000 genomes]
rs174649	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs174718	1.00[JPT][hapmap]
rs1800540	0.85[ASN][1000 genomes]
rs2008880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530660	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2857634	0.80[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs457930	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs465736	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs467669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs467768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs468563	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs469189	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823046	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823048	0.85[ASN][1000 genomes]
rs5752917	1.00[JPT][hapmap]
rs5763347	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763348	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6006219	1.00[JPT][hapmap]
rs6006225	0.80[CEU][hapmap]
rs695776	0.81[EUR][1000 genomes]
rs73159014	1.00[ASN][1000 genomes]
rs737979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625852	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]

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	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5763315	NIPSNAP1	cis	parietal	SCAN
rs5763315	SEC14L4	cis	cerebellum	SCAN
rs5763315	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs5763315	SGSM1	cis	cerebellum	SCAN
rs5763315	C22orf13	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29898200-29947400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:29900400-29949200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr22:29901000-29947600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr22:29901200-29941600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr22:29901200-29945600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr22:29901400-29945800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr22:29902400-29941200	Strong transcription	Placenta	Placenta
8	chr22:29902600-29949000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr22:29910000-29947800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr22:29910600-29947800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr22:29911200-29947000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr22:29911400-29945400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr22:29913600-29949200	Weak transcription	Right Atrium	heart
14	chr22:29917800-29942400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr22:29918000-29948000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr22:29919000-29946600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr22:29919200-29941000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr22:29919200-29946600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr22:29919200-29946800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr22:29919400-29941000	Strong transcription	NH-A	brain
21	chr22:29919400-29941200	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr22:29919400-29941600	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr22:29919400-29941600	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr22:29919400-29941800	Strong transcription	Primary T cells from cord blood	blood
25	chr22:29919400-29942000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr22:29919400-29942000	Strong transcription	Fetal Brain Female	brain
27	chr22:29919400-29942200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr22:29919400-29942200	Strong transcription	Dnd41	blood
29	chr22:29919400-29942400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr22:29919400-29942400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr22:29919400-29942400	Strong transcription	Osteobl	bone
32	chr22:29919400-29945200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr22:29919400-29946200	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr22:29919400-29946600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr22:29919400-29946800	Strong transcription	Fetal Muscle Leg	muscle
36	chr22:29919400-29947000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr22:29919400-29947000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr22:29919600-29942200	Strong transcription	Brain Hippocampus Middle	brain
39	chr22:29919600-29945400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr22:29919600-29945400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr22:29919800-29941200	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr22:29919800-29945800	Strong transcription	Thymus	Thymus
43	chr22:29921000-29945400	Strong transcription	Liver	Liver
44	chr22:29921200-29942000	Strong transcription	Fetal Intestine Large	intestine
45	chr22:29921800-29942200	Strong transcription	Adipose Nuclei	Adipose
46	chr22:29925000-29949200	Weak transcription	Small Intestine	intestine
47	chr22:29925600-29946600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr22:29925800-29947000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr22:29925800-29948800	Weak transcription	Stomach Mucosa	stomach
50	chr22:29926600-29942200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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