Variant report

Variant	rs2530661
Chromosome Location	chr22:30024263-30024264
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs2007668	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2024117	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2052023	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2079647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2283860	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2527334	0.94[JPT][hapmap]
rs2527335	0.93[JPT][hapmap]
rs2530662	0.94[JPT][hapmap]
rs2531844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2857638	0.94[JPT][hapmap]
rs2857643	0.94[JPT][hapmap]
rs2857647	0.94[JPT][hapmap]
rs456300	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[EUR][1000 genomes]
rs465938	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[EUR][1000 genomes]
rs467812	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs468150	0.83[EUR][1000 genomes]
rs468217	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs468851	0.83[EUR][1000 genomes]
rs468902	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs468986	0.83[EUR][1000 genomes]
rs5763296	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs5763302	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs5763304	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs5763378	0.93[JPT][hapmap]
rs6006179	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6361	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[EUR][1000 genomes]
rs6519793	0.94[JPT][hapmap]
rs695399	0.85[EUR][1000 genomes]
rs737976	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs737977	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs8140060	0.87[JPT][hapmap]
rs9613968	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9613976	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv817417	chr22:29998464-30035142	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2530661	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs2530661	NIPSNAP1	cis	Artery Tibial	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30000400-30026600	Weak transcription	Gastric	stomach
2	chr22:30003800-30032800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr22:30011800-30026200	Weak transcription	Fetal Stomach	stomach
4	chr22:30014400-30085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr22:30014800-30032000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr22:30015400-30026400	Weak transcription	Brain Anterior Caudate	brain
7	chr22:30018000-30026400	Weak transcription	Right Atrium	heart
8	chr22:30018000-30069200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr22:30018200-30024400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr22:30018200-30024600	Enhancers	HMEC	breast
11	chr22:30018400-30025000	Weak transcription	Fetal Intestine Small	intestine
12	chr22:30018400-30025800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr22:30018400-30033400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr22:30018600-30024400	Enhancers	NHLF	lung
15	chr22:30018800-30024400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr22:30019000-30024400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr22:30019600-30026800	Enhancers	Dnd41	blood
18	chr22:30019600-30029400	Weak transcription	Esophagus	oesophagus
19	chr22:30019800-30033800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr22:30020000-30024400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr22:30020000-30026400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr22:30020200-30029400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr22:30020200-30033200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr22:30020200-30033600	Weak transcription	GM12878-XiMat	blood
25	chr22:30020200-30057000	Weak transcription	Psoas Muscle	Psoas
26	chr22:30020200-30064200	Weak transcription	Small Intestine	intestine
27	chr22:30020400-30032800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr22:30020400-30033400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr22:30020600-30026400	Weak transcription	Right Ventricle	heart
30	chr22:30020600-30028200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr22:30020600-30029200	Weak transcription	Thymus	Thymus
32	chr22:30020600-30032800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr22:30020800-30029200	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
35	chr22:30021200-30026400	Weak transcription	Left Ventricle	heart
36	chr22:30021200-30026400	Weak transcription	Spleen	Spleen
37	chr22:30021200-30026600	Weak transcription	Lung	lung
38	chr22:30021200-30029400	Weak transcription	Fetal Muscle Leg	muscle
39	chr22:30021200-30033200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr22:30021600-30025200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr22:30021800-30029200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr22:30021800-30032800	Weak transcription	Liver	Liver
43	chr22:30021800-30041600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr22:30022000-30025000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr22:30022000-30025600	Weak transcription	Fetal Kidney	kidney
46	chr22:30022000-30028400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr22:30022000-30028400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr22:30022000-30033400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr22:30022000-30037200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr22:30022000-30038400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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