Variant report

Variant	rs737977
Chromosome Location	chr22:29919830-29919831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29876640..29878874-chr22:29919748..29922123,2	K562	blood:
2	chr22:29700578..29702858-chr22:29919367..29920901,2	MCF-7	breast:
3	chr22:29875265..29878874-chr22:29919290..29922123,3	K562	blood:
4	chr22:29907526..29909424-chr22:29918736..29921432,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100285	Chromatin interaction
ENSG00000185340	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2007668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052023	0.80[EUR][1000 genomes]
rs2079647	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2283860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527334	0.94[JPT][hapmap]
rs2527335	0.93[JPT][hapmap]
rs2530661	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2530662	0.94[JPT][hapmap]
rs2531844	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2857638	0.94[JPT][hapmap]
rs2857643	0.94[JPT][hapmap]
rs2857647	0.94[JPT][hapmap]
rs456300	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs465938	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs467812	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]
rs468150	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs468217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs468221	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs468851	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs468902	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs468986	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5763294	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763295	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763302	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5763304	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5763378	0.93[JPT][hapmap]
rs6006179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6361	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6519793	0.94[JPT][hapmap]
rs695399	0.87[EUR][1000 genomes]
rs737976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8140060	0.87[JPT][hapmap]
rs9613968	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9613976	0.82[CEU][hapmap];0.89[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs737977	NIPSNAP1	cis	Artery Tibial	GTEx
rs737977	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29897600-29934600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr22:29898200-29947400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:29900400-29929000	Strong transcription	Fetal Stomach	stomach
4	chr22:29900400-29949200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr22:29900800-29929000	Strong transcription	Fetal Intestine Small	intestine
6	chr22:29900800-29930600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr22:29901000-29947600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr22:29901200-29925200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr22:29901200-29929600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr22:29901200-29941600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr22:29901200-29945600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr22:29901400-29937200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr22:29901400-29945800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr22:29902200-29937000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr22:29902400-29923800	Strong transcription	Lung	lung
16	chr22:29902400-29930000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr22:29902400-29941200	Strong transcription	Placenta	Placenta
18	chr22:29902600-29949000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr22:29903600-29931000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr22:29904600-29927600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr22:29910000-29947800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr22:29910600-29947800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr22:29910800-29937000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr22:29911200-29921400	Strong transcription	Adipose Nuclei	Adipose
25	chr22:29911200-29938000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr22:29911200-29947000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr22:29911400-29930400	Strong transcription	HSMM	muscle
28	chr22:29911400-29945400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr22:29913600-29925800	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr22:29913600-29949200	Weak transcription	Right Atrium	heart
31	chr22:29914000-29929600	Weak transcription	Fetal Heart	heart
32	chr22:29914800-29921400	Strong transcription	Hela-S3	cervix
33	chr22:29915000-29924800	Weak transcription	Stomach Mucosa	stomach
34	chr22:29915400-29920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr22:29915400-29920600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr22:29915600-29920000	Weak transcription	Small Intestine	intestine
37	chr22:29916400-29926200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr22:29917400-29920000	Weak transcription	Right Ventricle	heart
39	chr22:29917400-29925000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr22:29917800-29920000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr22:29917800-29920000	Weak transcription	Gastric	stomach
42	chr22:29917800-29920600	Weak transcription	Colon Smooth Muscle	Colon
43	chr22:29917800-29921000	Weak transcription	Fetal Brain Male	brain
44	chr22:29917800-29921600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr22:29917800-29942400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr22:29918000-29920000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr22:29918000-29920000	Weak transcription	Primary B cells from cord blood	blood
48	chr22:29918000-29920000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr22:29918000-29920000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr22:29918000-29920000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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