Variant report

Variant	rs2530672
Chromosome Location	chr22:30056185-30056186
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1034880	0.86[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes]
rs1476757	0.86[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs2071622	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2245185	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2245415	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2252472	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2252587	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267150	0.86[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes]
rs2267151	0.85[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes]
rs2283863	0.86[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes]
rs2283864	0.89[AFR][1000 genomes]
rs2527337	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2530667	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2530668	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2530669	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2530670	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2530673	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2530675	0.86[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs2530676	0.90[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes]
rs2531850	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2857637	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2857639	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2857640	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857641	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2857642	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857645	0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2857648	0.85[JPT][hapmap]
rs2857650	0.86[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2857651	0.80[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes]
rs5752953	0.88[AFR][1000 genomes]
rs5763409	0.91[AFR][1000 genomes]
rs5763422	0.92[AFR][1000 genomes]
rs5763431	0.88[AFR][1000 genomes]
rs7291645	0.85[JPT][hapmap]
rs737931	0.86[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes]
rs9608806	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	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
6	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2530672	NIPSNAP1	cis	multi-tissue	Pritchard
rs2530672	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30014400-30085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30018000-30069200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:30020200-30057000	Weak transcription	Psoas Muscle	Psoas
4	chr22:30020200-30064200	Weak transcription	Small Intestine	intestine
5	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
6	chr22:30027600-30057200	Weak transcription	Brain Hippocampus Middle	brain
7	chr22:30032200-30057000	Weak transcription	Colonic Mucosa	Colon
8	chr22:30032200-30070000	Weak transcription	Fetal Brain Male	brain
9	chr22:30034400-30060400	Weak transcription	K562	blood
10	chr22:30035400-30060800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr22:30035600-30057200	Weak transcription	Placenta	Placenta
12	chr22:30037200-30064200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr22:30038200-30057000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr22:30038400-30060600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr22:30038800-30057000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr22:30038800-30069800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr22:30039000-30068000	Weak transcription	Hela-S3	cervix
18	chr22:30039200-30056200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr22:30042200-30057200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr22:30043800-30064000	Weak transcription	Fetal Heart	heart
21	chr22:30044800-30058200	Weak transcription	Right Ventricle	heart
22	chr22:30044800-30059600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr22:30045000-30060600	Weak transcription	Brain Substantia Nigra	brain
24	chr22:30047400-30056200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr22:30047800-30057600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr22:30048000-30064000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr22:30048000-30064200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr22:30048200-30057200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr22:30049600-30061000	Strong transcription	Dnd41	blood
30	chr22:30049600-30062000	Strong transcription	HSMM	muscle
31	chr22:30049800-30057400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr22:30050000-30056600	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr22:30050000-30062400	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr22:30050200-30061800	Strong transcription	Primary T cells from cord blood	blood
35	chr22:30050200-30075000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr22:30050200-30084800	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr22:30050400-30057000	Strong transcription	Osteobl	bone
38	chr22:30050400-30061200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr22:30050400-30061800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr22:30050400-30062800	Strong transcription	Liver	Liver
41	chr22:30050400-30084400	Strong transcription	Left Ventricle	heart
42	chr22:30050400-30093000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr22:30050600-30057200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr22:30050600-30062000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr22:30050800-30061000	Strong transcription	Adipose Nuclei	Adipose
46	chr22:30050800-30061400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr22:30050800-30084800	Strong transcription	Thymus	Thymus
48	chr22:30051000-30083600	Strong transcription	Fetal Muscle Leg	muscle
49	chr22:30051000-30085400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr22:30051200-30057800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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