Variant report

Variant	rs2301402
Chromosome Location	chr22:30234045-30234046
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr22:30233831-30234581	HepG2	liver:	n/a	n/a
2	POLR2A	chr22:30233945-30234739	MCF-7	breast:	n/a	n/a
3	MAX	chr22:30233859-30234627	Hela-S3	cervix:	n/a	chr22:30233934-30233943
4	RFX5	chr22:30233969-30234660	Hela-S3	cervix:	n/a	n/a
5	ETS1	chr22:30233995-30234459	K562	blood:	n/a	chr22:30234282-30234296 chr22:30234301-30234312 chr22:30234282-30234291
6	CHD2	chr22:30233825-30234564	Hela-S3	cervix:	n/a	n/a
7	ZNF143	chr22:30233692-30234551	Hela-S3	cervix:	n/a	n/a
8	MAX	chr22:30233789-30234682	ECC-1	luminal epithelium:	n/a	chr22:30233934-30233943
9	POLR2A	chr22:30233948-30234858	GM12878	blood:	n/a	n/a
10	YY1	chr22:30233833-30234554	K562	blood:	n/a	chr22:30234301-30234310
11	CTCF	chr22:30233920-30234070	GM12867	blood:	n/a	n/a
12	ELF1	chr22:30233793-30234768	MCF-7	breast:	n/a	chr22:30234278-30234291 chr22:30234245-30234258
13	NR2F2	chr22:30233959-30234662	K562	blood:	n/a	n/a
14	TAF1	chr22:30234017-30234544	H1-neurons	neurons:	n/a	n/a
15	CHD2	chr22:30233977-30234614	K562	blood:	n/a	n/a
16	ATF2	chr22:30234033-30234573	GM12878	blood:	n/a	n/a
17	POLR2A	chr22:30233855-30234827	HUVEC	blood vessel:	n/a	n/a
18	HEY1	chr22:30233982-30234739	HepG2	liver:	n/a	n/a
19	CTCF	chr22:30234040-30234190	GM12871	blood:	n/a	n/a
20	POLR2A	chr22:30233957-30234790	H1-hESC	embryonic stem cell:	n/a	n/a
21	ELF1	chr22:30233873-30234643	GM12878	blood:	n/a	chr22:30234278-30234291 chr22:30234245-30234258
22	POLR2A	chr22:30233837-30234778	GM12892	blood:	n/a	n/a
23	POLR2A	chr22:30234015-30234468	K562	blood:	n/a	n/a
24	CREB1	chr22:30234006-30234517	A549	lung:	n/a	n/a
25	POLR2A	chr22:30233958-30234631	HCT-116	colon:	n/a	n/a
26	RCOR1	chr22:30233682-30234144	K562	blood:	n/a	n/a
27	GABPA	chr22:30233852-30234617	MCF-7	breast:	n/a	chr22:30234301-30234310
28	POLR2A	chr22:30233978-30234585	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr22:30233846-30234727	GM12891	blood:	n/a	n/a
30	CTCF	chr22:30233920-30234070	HBMEC	blood vessel:	n/a	n/a
31	MAZ	chr22:30233907-30234608	HepG2	liver:	n/a	chr22:30233934-30233943
32	POLR2A	chr22:30233907-30234733	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr22:30233796-30234703	H1-neurons	neurons:	n/a	n/a
34	REST	chr22:30233464-30234918	H1-neurons	neurons:	n/a	chr22:30233992-30234005
35	GABPA	chr22:30233745-30234620	A549	lung:	n/a	chr22:30234301-30234310
36	CTCF	chr22:30233980-30234130	HCPEpiC	choroid plexus:	n/a	n/a
37	GABPA	chr22:30233731-30234472	K562	blood:	n/a	chr22:30234301-30234310
38	POLR2A	chr22:30233997-30234723	SK-N-SH	brain:	n/a	n/a
39	CTCF	chr22:30233900-30234050	HMEC	breast:	n/a	n/a
40	POLR2A	chr22:30233869-30234833	GM12892	blood:	n/a	n/a
41	TBP	chr22:30234037-30234654	K562	blood:	n/a	n/a
42	ELF1	chr22:30233911-30234729	SK-N-SH	brain:	n/a	chr22:30234278-30234291 chr22:30234245-30234258
43	TAF1	chr22:30234001-30234730	ECC-1	luminal epithelium:	n/a	n/a
44	ELF1	chr22:30233928-30234659	HepG2	liver:	n/a	chr22:30234278-30234291 chr22:30234245-30234258
45	MAX	chr22:30233915-30234556	NB4	blood:	n/a	chr22:30233934-30233943
46	POLR2A	chr22:30233878-30234752	Hela-S3	cervix:	n/a	n/a
47	HCFC1	chr22:30233524-30234884	Hela-S3	cervix:	n/a	n/a
48	SIN3AK20	chr22:30233858-30234510	PANC-1	pancreas:	n/a	n/a
49	POLR2A	chr22:30233980-30234661	PANC-1	pancreas:	n/a	n/a
50	POLR2A	chr22:30233897-30234799	GM18951	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:30216228..30218392-chr22:30231989..30234163,2	K562	blood:
2	chr16:46723531..46724116-chr22:30233901..30234633,2	Hela-S3	cervix:
3	chr22:30232954..30235817-chr22:30277750..30279574,2	MCF-7	breast:
4	chr22:30225765..30230715-chr22:30232604..30236000,6	K562	blood:
5	chr22:30221897..30227952-chr22:30230604..30235599,8	MCF-7	breast:
6	chr22:30199503..30202747-chr22:30231620..30235442,3	MCF-7	breast:
7	chr22:30228546..30230856-chr22:30232707..30235317,4	MCF-7	breast:
8	chr22:30232501..30234053-chr22:30238394..30240454,2	K562	blood:
9	chr22:30228718..30231367-chr22:30232651..30236541,5	K562	blood:
10	chr22:30224439..30228420-chr22:30233600..30235751,3	K562	blood:
11	chr22:30226725..30230027-chr22:30233173..30235923,3	MCF-7	breast:
12	chr22:30162371..30164035-chr22:30233277..30234908,2	MCF-7	breast:
13	chr22:30209515..30211458-chr22:30232926..30235230,2	K562	blood:

Variant related genes	Relation type
ASCC2	TF binding region
ENSG00000184076	Chromatin interaction
ENSG00000100325	Chromatin interaction
ENSG00000100330	Chromatin interaction
ENSG00000100319	Chromatin interaction
ENSG00000091651	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1138120	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs131262	0.89[CEU][hapmap]
rs131293	0.87[AMR][1000 genomes]
rs131295	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs140095	0.80[AMR][1000 genomes]
rs140118	0.89[CEU][hapmap]
rs140124	0.89[CEU][hapmap]
rs140145	1.00[CEU][hapmap];0.92[AMR][1000 genomes]
rs140147	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs140149	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs140150	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17462966	0.86[CHB][hapmap]
rs17711377	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2007446	0.92[CEU][hapmap]
rs2057882	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2074706	0.96[CEU][hapmap];0.91[AMR][1000 genomes]
rs2074707	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2079338	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs249398	0.80[CEU][hapmap]
rs28749829	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36576	0.82[CEU][hapmap]
rs3788417	0.86[CHB][hapmap]
rs3958027	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs41168	0.92[CEU][hapmap]
rs41171	0.86[CEU][hapmap]
rs41173	0.86[CEU][hapmap]
rs5752961	0.80[CEU][hapmap]
rs5752964	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5752978	0.89[CEU][hapmap]
rs5763512	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5997529	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5997530	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5997535	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5997549	0.83[AMR][1000 genomes]
rs6006267	0.85[CEU][hapmap]
rs6006274	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6006288	0.83[AMR][1000 genomes]
rs713656	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs713657	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7287434	0.85[AMR][1000 genomes]
rs737911	0.89[CEU][hapmap]
rs737945	0.86[CEU][hapmap]
rs740041	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs81800	0.82[CEU][hapmap]
rs9306465	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9306468	0.86[CEU][hapmap]
rs9614077	0.91[AMR][1000 genomes];0.82[EUR][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
rs2301402	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	chr22:30232000-30234600	Active TSS	GM12878-XiMat	blood
2	chr22:30233000-30234400	Active TSS	Muscle Satellite Cultured Cells	--
3	chr22:30233000-30234600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:30233000-30234800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr22:30233000-30234800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr22:30233200-30234400	Active TSS	HSMM	muscle
7	chr22:30233200-30234600	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr22:30233200-30234600	Active TSS	Stomach Mucosa	stomach
9	chr22:30233200-30234600	Active TSS	A549	lung
10	chr22:30233200-30234600	Active TSS	NHLF	lung
11	chr22:30233200-30234800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr22:30233400-30234200	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr22:30233400-30234200	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr22:30233400-30234200	Flanking Active TSS	Fetal Muscle Trunk	muscle
15	chr22:30233400-30234200	Flanking Active TSS	Thymus	Thymus
16	chr22:30233400-30234400	Active TSS	Brain Germinal Matrix	brain
17	chr22:30233400-30234600	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr22:30233400-30234600	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr22:30233400-30234600	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr22:30233400-30234600	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr22:30233400-30234600	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr22:30233400-30234600	Bivalent/Poised TSS	HepG2	liver
23	chr22:30233400-30234600	Active TSS	HSMMtube	muscle
24	chr22:30233400-30234600	Active TSS	NHDF-Ad	bronchial
25	chr22:30233400-30234800	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr22:30233400-30234800	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr22:30233400-30235000	Active TSS	Fetal Kidney	kidney
28	chr22:30233600-30234200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr22:30233600-30234400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr22:30233600-30234400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
31	chr22:30233600-30234600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr22:30233600-30234600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr22:30233600-30234600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr22:30233600-30234600	Active TSS	Brain Hippocampus Middle	brain
35	chr22:30233600-30234600	Active TSS	Left Ventricle	heart
36	chr22:30233600-30234600	Active TSS	Lung	lung
37	chr22:30233600-30234600	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr22:30233600-30234800	Active TSS	H9 Cell Line	embryonic stem cell
39	chr22:30233600-30234800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr22:30233600-30234800	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr22:30233600-30234800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr22:30233600-30234800	Active TSS	Aorta	Aorta
43	chr22:30233600-30235000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr22:30233800-30234200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
45	chr22:30233800-30234200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
46	chr22:30233800-30234200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr22:30233800-30234400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr22:30233800-30234400	Active TSS	Liver	Liver
49	chr22:30233800-30234400	Active TSS	Gastric	stomach
50	chr22:30233800-30234400	Active TSS	NHEK	skin

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