Variant report

Variant	rs740041
Chromosome Location	chr22:30200099-30200100
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30199847..30201842-chr22:30205900..30208227,2	MCF-7	breast:
2	chr22:30199503..30202747-chr22:30231620..30235442,3	MCF-7	breast:
3	chr22:30198973..30201297-chr22:30207957..30210741,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100325	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs105311	0.87[CHB][hapmap]
rs1138120	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs131260	0.88[CHB][hapmap]
rs131262	0.86[CEU][hapmap];0.88[CHB][hapmap]
rs131269	0.81[AMR][1000 genomes]
rs131271	0.87[CHB][hapmap]
rs131272	0.87[CHB][hapmap]
rs131273	0.87[CHB][hapmap]
rs131274	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs131277	0.88[CHB][hapmap]
rs131279	0.88[CHB][hapmap]
rs131282	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs131284	0.84[CHB][hapmap]
rs131285	0.87[CHB][hapmap]
rs131289	0.81[AMR][1000 genomes]
rs131293	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs131295	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs131301	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs140095	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs140096	0.88[CHB][hapmap]
rs140097	0.83[CHB][hapmap]
rs140099	0.84[CHB][hapmap]
rs140100	0.88[CHB][hapmap]
rs140101	0.87[CHB][hapmap]
rs140102	0.88[CHB][hapmap]
rs140104	0.83[CHB][hapmap]
rs140106	0.84[CHB][hapmap]
rs140107	0.88[CHB][hapmap]
rs140110	0.88[CHB][hapmap]
rs140111	0.88[CHB][hapmap]
rs140113	0.84[CHB][hapmap]
rs140114	0.83[CHB][hapmap]
rs140118	0.86[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes]
rs140119	0.84[CHB][hapmap]
rs140120	0.87[CHB][hapmap]
rs140121	0.84[CHB][hapmap]
rs140123	0.87[CHB][hapmap]
rs140124	0.85[CEU][hapmap];0.87[CHB][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs140126	0.83[CHB][hapmap]
rs140128	0.84[CHB][hapmap]
rs140129	0.87[CHB][hapmap]
rs140133	0.87[CHB][hapmap]
rs140145	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140147	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs140149	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs140150	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17711377	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2007446	0.89[CEU][hapmap]
rs2057882	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2074706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2079338	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2301402	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs249398	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs28749829	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36574	0.94[ASN][1000 genomes]
rs36576	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3958027	0.84[AMR][1000 genomes]
rs5752961	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5752964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752978	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs5763512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997529	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5997530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997535	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997549	0.84[AMR][1000 genomes]
rs6006267	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs6006274	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6006288	0.84[AMR][1000 genomes]
rs713656	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs713657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs737911	0.85[CEU][hapmap]
rs737945	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs81800	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9306465	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9306468	0.83[CEU][hapmap]
rs9614055	1.00[ASN][1000 genomes]
rs9614077	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs740041	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30177600-30233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30182200-30217000	Strong transcription	Fetal Intestine Small	intestine
3	chr22:30182200-30222200	Strong transcription	Thymus	Thymus
4	chr22:30182800-30204600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr22:30182800-30204800	Strong transcription	Fetal Brain Female	brain
6	chr22:30182800-30232200	Strong transcription	Primary T cells from cord blood	blood
7	chr22:30182800-30232200	Strong transcription	Fetal Stomach	stomach
8	chr22:30183000-30221400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr22:30183200-30230800	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr22:30183400-30204800	Strong transcription	Brain Germinal Matrix	brain
11	chr22:30183400-30224000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr22:30183400-30230800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr22:30183800-30204800	Strong transcription	Ovary	ovary
14	chr22:30183800-30205000	Strong transcription	Fetal Intestine Large	intestine
15	chr22:30183800-30205200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr22:30183800-30224000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr22:30183800-30232200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr22:30184000-30204800	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr22:30184000-30222200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr22:30189600-30201000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr22:30189600-30201800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr22:30189800-30201800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr22:30191000-30222200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr22:30193400-30217200	Strong transcription	Fetal Thymus	thymus
25	chr22:30194200-30212200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr22:30195200-30204600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr22:30195200-30204600	Strong transcription	Brain Anterior Caudate	brain
28	chr22:30195200-30204800	Strong transcription	Rectal Smooth Muscle	rectum
29	chr22:30195200-30205000	Strong transcription	Brain Cingulate Gyrus	brain
30	chr22:30195400-30203600	Strong transcription	Primary hematopoietic stem cells	blood
31	chr22:30195400-30205400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr22:30195400-30222000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr22:30195400-30222200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr22:30195600-30204600	Strong transcription	GM12878-XiMat	blood
35	chr22:30195600-30205000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr22:30195600-30208200	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr22:30195800-30200800	Weak transcription	NHDF-Ad	bronchial
38	chr22:30195800-30201600	Strong transcription	Stomach Smooth Muscle	stomach
39	chr22:30195800-30204600	Strong transcription	Primary B cells from cord blood	blood
40	chr22:30195800-30204600	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr22:30195800-30204800	Strong transcription	Brain Angular Gyrus	brain
42	chr22:30195800-30204800	Strong transcription	Colonic Mucosa	Colon
43	chr22:30195800-30205000	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr22:30196000-30205000	Strong transcription	Aorta	Aorta
45	chr22:30196000-30205000	Strong transcription	Brain Hippocampus Middle	brain
46	chr22:30196000-30212000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr22:30196000-30217000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr22:30196200-30202400	Strong transcription	Fetal Brain Male	brain
49	chr22:30196200-30204400	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr22:30196200-30204600	Strong transcription	Brain Substantia Nigra	brain

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