Variant report

Variant	rs467812
Chromosome Location	chr22:29940949-29940950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29940656..29942248-chr22:29948423..29951166,2	MCF-7	breast:
2	chr22:29873715..29877046-chr22:29940798..29944268,3	K562	blood:
3	chr22:29929556..29932082-chr22:29939734..29941953,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100285	Chromatin interaction
ENSG00000234208	Chromatin interaction
ENSG00000225465	Chromatin interaction
ENSG00000100296	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs2007668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2024117	0.82[EUR][1000 genomes]
rs2052023	0.83[EUR][1000 genomes]
rs2079647	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2283860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2527334	0.93[JPT][hapmap]
rs2527335	0.93[JPT][hapmap]
rs2530661	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2530662	0.93[JPT][hapmap]
rs2531844	0.82[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs2857638	0.93[JPT][hapmap]
rs2857643	0.93[JPT][hapmap]
rs2857647	0.93[JPT][hapmap]
rs2881995	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs456300	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs465938	0.89[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs468150	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs468217	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs468221	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs468851	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs468902	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs468986	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763294	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5763295	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5763296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5763302	0.88[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763304	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763378	0.93[JPT][hapmap]
rs6006179	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6361	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6519793	0.93[JPT][hapmap]
rs695399	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs737976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs737977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8140060	0.86[JPT][hapmap]
rs9613968	0.88[ASW][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap];0.82[ASN][1000 genomes]
rs9613976	0.82[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs467812	NIPSNAP1	cis	Artery Tibial	GTEx
rs467812	NIPSNAP1	cis	cerebellum	SCAN
rs467812	THOC5	cis	parietal	SCAN
rs467812	NIPSNAP1	cis	parietal	SCAN
rs467812	PITPNB	cis	cerebellum	SCAN
rs467812	CRYBB3	cis	parietal	SCAN
rs467812	THOC5	cis	cerebellum	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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