Variant report

Variant	rs6006274
Chromosome Location	chr22:30232843-30232844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr22:30232661-30233010	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr22:30232820-30232970	GM12867	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30216228..30218392-chr22:30231989..30234163,2	K562	blood:
2	chr22:30225765..30230715-chr22:30232604..30236000,6	K562	blood:
3	chr22:30221897..30227952-chr22:30230604..30235599,8	MCF-7	breast:
4	chr22:30199503..30202747-chr22:30231620..30235442,3	MCF-7	breast:
5	chr22:30228546..30230856-chr22:30232707..30235317,4	MCF-7	breast:
6	chr22:30232501..30234053-chr22:30238394..30240454,2	K562	blood:
7	chr22:30228718..30231367-chr22:30232651..30236541,5	K562	blood:

No data

Variant related genes	Relation type
ASCC2	TF binding region
ENSG00000100325	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1138120	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs131293	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs131295	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs131301	0.91[ASN][1000 genomes]
rs140095	0.82[AMR][1000 genomes]
rs140145	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs140147	0.88[AMR][1000 genomes]
rs140149	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs140150	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17711377	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2057882	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2074706	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2074707	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2079338	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2301402	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs249398	0.94[ASN][1000 genomes]
rs28749829	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36574	0.90[ASN][1000 genomes]
rs36576	0.94[ASN][1000 genomes]
rs3958027	0.87[AMR][1000 genomes]
rs5752961	0.92[ASN][1000 genomes]
rs5752964	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5752978	0.83[AMR][1000 genomes]
rs5763512	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5997529	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5997530	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997535	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997549	0.87[AMR][1000 genomes]
rs6006288	0.87[AMR][1000 genomes]
rs713656	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs713657	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7287434	0.82[AMR][1000 genomes]
rs740041	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs81800	0.92[ASN][1000 genomes]
rs9306465	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9614055	0.92[ASN][1000 genomes]
rs9614077	0.87[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
rs6006274	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	chr22:30177600-30233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30203600-30233400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr22:30208800-30233400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:30209800-30233600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr22:30215200-30233200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr22:30218400-30233000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr22:30218600-30233400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr22:30219600-30233400	Weak transcription	Fetal Kidney	kidney
9	chr22:30221400-30233400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr22:30221600-30233400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr22:30221800-30233400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr22:30221800-30233600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr22:30222000-30233600	Weak transcription	Small Intestine	intestine
14	chr22:30224200-30233200	Weak transcription	Right Atrium	heart
15	chr22:30224800-30233000	Weak transcription	Pancreas	Pancrea
16	chr22:30227600-30233400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr22:30228000-30233400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr22:30228000-30233400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr22:30228200-30233000	Weak transcription	Gastric	stomach
20	chr22:30228400-30233000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr22:30228400-30233000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr22:30228400-30233400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr22:30228400-30233400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr22:30229000-30233600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr22:30229400-30233400	Weak transcription	Brain Angular Gyrus	brain
26	chr22:30229600-30233400	Weak transcription	Fetal Lung	lung
27	chr22:30229600-30233400	Weak transcription	HSMMtube	muscle
28	chr22:30229800-30233000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr22:30229800-30233000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr22:30230000-30233200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr22:30230000-30233400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr22:30230200-30233400	Weak transcription	NHDF-Ad	bronchial
33	chr22:30230400-30233000	Enhancers	Stomach Mucosa	stomach
34	chr22:30230400-30233400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr22:30230400-30233400	Weak transcription	Placenta	Placenta
36	chr22:30230400-30233600	Weak transcription	Aorta	Aorta
37	chr22:30230600-30233000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr22:30230600-30233000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr22:30230600-30233000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr22:30230600-30233000	Weak transcription	Brain Substantia Nigra	brain
41	chr22:30230600-30233000	Weak transcription	Fetal Thymus	thymus
42	chr22:30230600-30233000	Weak transcription	Thymus	Thymus
43	chr22:30230600-30233000	Weak transcription	HSMM	muscle
44	chr22:30230600-30233400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr22:30230600-30233600	Weak transcription	Esophagus	oesophagus
46	chr22:30230800-30233400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr22:30230800-30233400	Weak transcription	Fetal Heart	heart
48	chr22:30231000-30233000	Weak transcription	Primary B cells from cord blood	blood
49	chr22:30231000-30233000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr22:30231000-30233000	Weak transcription	Brain Germinal Matrix	brain

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