Variant report

Variant	rs2991976
Chromosome Location	chr1:46048489-46048490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:32)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr1:46047993-46048726	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:46047917-46048544	GM12892	blood:	n/a	n/a
3	PAX5	chr1:46048099-46048533	GM12878	blood:	n/a	chr1:46048368-46048387
4	SPI1	chr1:46048115-46048490	GM12878	blood:	n/a	n/a
5	PAX5	chr1:46048062-46048641	GM12878	blood:	n/a	chr1:46048368-46048387
6	POLR2A	chr1:46048041-46048574	Raji	blood:	n/a	n/a
7	ZNF384	chr1:46048097-46048521	GM12878	blood:	n/a	n/a
8	MTA3	chr1:46047827-46048548	GM12878	blood:	n/a	n/a
9	PAX5	chr1:46048204-46048531	GM12891	blood:	n/a	chr1:46048368-46048387
10	PAX5	chr1:46048140-46048687	GM12878	blood:	n/a	chr1:46048368-46048387

No data

(count:32 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46012797..46020877-chr1:46047985..46055272,23	K562	blood:
2	chr1:46047808..46051262-chr1:46767344..46769900,3	K562	blood:
3	chr1:46048444..46052841-chr10:129795145..129798145,4	K562	blood:
4	chr1:45185636..45188407-chr1:46047872..46052515,5	K562	blood:
5	chr1:46048178..46050215-chr1:46089233..46091590,2	K562	blood:
6	chr1:46047578..46050794-chr1:46077080..46080053,4	K562	blood:
7	chr1:45283391..45288738-chr1:46048072..46051277,6	K562	blood:
8	chr1:45963397..45969763-chr1:46047572..46053150,23	K562	blood:
9	chr1:45194369..45197773-chr1:46046767..46051199,5	K562	blood:
10	chr1:45986151..45989227-chr1:46047437..46050636,3	MCF-7	breast:
11	chr1:45980210..45995142-chr1:46046095..46057139,89	K562	blood:
12	chr1:45803780..45809046-chr1:46047811..46052394,14	K562	blood:
13	chr1:45974971..45980027-chr1:46048272..46053531,9	K562	blood:
14	chr1:46026984..46033199-chr1:46047562..46051151,12	K562	blood:
15	chr1:46048446..46052403-chr1:46150752..46155740,15	K562	blood:
16	chr1:45186130..45188407-chr1:46047872..46051720,5	K562	blood:
17	chr1:46048335..46051372-chr1:46110517..46113642,3	K562	blood:
18	chr1:45970173..45973097-chr1:46047655..46049258,2	K562	blood:
19	chr1:45477030..45479805-chr1:46047527..46050763,5	K562	blood:
20	chr1:46034190..46037574-chr1:46047982..46052662,9	K562	blood:
21	chr1:46048069..46054740-chr1:46150080..46155979,19	K562	blood:
22	chr1:45963437..45971807-chr1:46047572..46053150,22	K562	blood:
23	chr1:45195288..45198728-chr1:46046767..46051124,6	K562	blood:
24	chr1:45951915..45956979-chr1:46048471..46052743,8	K562	blood:
25	chr1:46041016..46043943-chr1:46047684..46049396,2	MCF-7	breast:
26	chr1:46012228..46018632-chr1:46046407..46053601,17	K562	blood:
27	chr1:45974558..45995867-chr1:46046173..46057010,94	K562	blood:
28	chr1:45284255..45286941-chr1:46048411..46051884,4	K562	blood:
29	chr1:45985173..45987673-chr1:46047489..46052049,5	MCF-7	breast:
30	chr1:45240107..45242701-chr1:46047468..46050316,4	K562	blood:
31	chr1:45240022..45242115-chr1:46048297..46050844,3	K562	blood:
32	chr1:45803780..45808811-chr1:46047553..46051220,11	K562	blood:

No data

Variant related genes	Relation type
NASP	TF binding region
ENSG00000200913	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000159588	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000070759	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000173660	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000132128	Chromatin interaction
ENSG00000132334	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000225447	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1084086	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11211142	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1250	0.81[EUR][1000 genomes]
rs12727696	0.80[ASN][1000 genomes]
rs1541131	0.83[EUR][1000 genomes]
rs1547924	0.83[EUR][1000 genomes]
rs1547925	0.82[EUR][1000 genomes]
rs1972410	0.82[EUR][1000 genomes]
rs2050376	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2088102	0.88[ASN][1000 genomes]
rs2152078	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2230658	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2230659	0.81[ASN][1000 genomes]
rs2253862	0.82[EUR][1000 genomes]
rs2275085	0.82[EUR][1000 genomes]
rs2275086	0.81[EUR][1000 genomes]
rs2934857	0.96[ASN][1000 genomes]
rs2934858	0.96[ASN][1000 genomes]
rs2991973	0.81[ASN][1000 genomes]
rs2991977	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2991978	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2991979	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2991981	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2991983	0.82[EUR][1000 genomes]
rs2991986	0.83[EUR][1000 genomes]
rs2991987	0.83[EUR][1000 genomes]
rs2991988	0.82[EUR][1000 genomes]
rs2991989	0.82[EUR][1000 genomes]
rs3014210	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3014212	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3014213	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3014216	0.94[ASN][1000 genomes]
rs3014218	0.85[ASN][1000 genomes]
rs3014219	0.83[ASN][1000 genomes]
rs3014235	0.80[EUR][1000 genomes]
rs3014236	0.81[EUR][1000 genomes]
rs3014239	0.83[EUR][1000 genomes]
rs3014240	0.82[EUR][1000 genomes]
rs3014245	0.82[EUR][1000 genomes]
rs3014246	0.82[EUR][1000 genomes]
rs3014249	0.82[EUR][1000 genomes]
rs3014251	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs518216	0.99[ASN][1000 genomes]
rs563799	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs659437	0.99[ASN][1000 genomes]
rs7545118	0.81[AMR][1000 genomes]
rs7547414	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
4	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
5	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
6	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
7	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
8	esv3342998	chr1:46035908-46066462	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS 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	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2991976	GPBP1L1	cis	Muscle Skeletal	GTEx
rs2991976	IPP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46032600-46049000	Weak transcription	Right Atrium	heart
2	chr1:46033000-46048800	Weak transcription	Fetal Brain Male	brain
3	chr1:46034200-46048800	Weak transcription	Stomach Mucosa	stomach
4	chr1:46035400-46048800	Weak transcription	Brain Substantia Nigra	brain
5	chr1:46035600-46048800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:46035800-46048800	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:46035800-46048800	Weak transcription	Hela-S3	cervix
8	chr1:46036200-46048800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:46036400-46048600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr1:46036400-46048800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:46036400-46048800	Weak transcription	Brain Germinal Matrix	brain
12	chr1:46036400-46049200	Weak transcription	Gastric	stomach
13	chr1:46036600-46048600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:46036600-46048600	Weak transcription	Lung	lung
15	chr1:46036600-46048800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:46036600-46048800	Weak transcription	Brain Anterior Caudate	brain
17	chr1:46036600-46048800	Weak transcription	Fetal Kidney	kidney
18	chr1:46036600-46048800	Weak transcription	Fetal Lung	lung
19	chr1:46036600-46048800	Weak transcription	Dnd41	blood
20	chr1:46036600-46048800	Weak transcription	HepG2	liver
21	chr1:46036800-46048800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:46036800-46048800	Weak transcription	Adipose Nuclei	Adipose
23	chr1:46036800-46048800	Weak transcription	Liver	Liver
24	chr1:46036800-46048800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:46036800-46048800	Weak transcription	Fetal Brain Female	brain
26	chr1:46036800-46048800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:46036800-46048800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:46036800-46048800	Weak transcription	Thymus	Thymus
29	chr1:46036800-46048800	Weak transcription	A549	lung
30	chr1:46036800-46048800	Weak transcription	NH-A	brain
31	chr1:46036800-46048800	Weak transcription	Osteobl	bone
32	chr1:46036800-46049000	Weak transcription	Primary T cells from cord blood	blood
33	chr1:46036800-46049200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:46037000-46048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:46037200-46048800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:46037400-46048600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:46037400-46048600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:46037400-46048800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:46037400-46048800	Weak transcription	Fetal Intestine Large	intestine
40	chr1:46039200-46048800	Weak transcription	Fetal Intestine Small	intestine
41	chr1:46039600-46049000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:46040000-46049000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:46040200-46049200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:46045400-46049200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:46047600-46048800	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr1:46047600-46048800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:46047600-46049000	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr1:46047600-46049000	Enhancers	Primary hematopoietic stem cells	blood
49	chr1:46048000-46048600	Enhancers	K562	blood
50	chr1:46048000-46048800	Enhancers	Primary T helper cells fromperipheralblood	blood

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