Variant report

Variant	rs2153608
Chromosome Location	chr1:45813941-45813942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45769536..45771577-chr1:45812790..45815177,2	K562	blood:
2	chr1:45475941..45478297-chr1:45813885..45816135,2	K562	blood:
3	chr1:45478794..45481756-chr1:45811013..45814397,3	K562	blood:
4	chr1:45813567..45816269-chr1:45828110..45830975,4	K562	blood:
5	chr1:45769560..45771577-chr1:45812920..45815177,2	K562	blood:
6	chr1:45813460..45816251-chr1:45955172..45957736,3	MCF-7	breast:
7	chr1:45813588..45815184-chr1:45986988..45988568,2	K562	blood:
8	chr1:45812595..45814836-chr1:46042720..46044656,2	K562	blood:
9	chr1:45259473..45261876-chr1:45813673..45815846,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000126088	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000070759	Chromatin interaction
ENSG00000117450	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1006216	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs1007858	0.81[EUR][1000 genomes]
rs1084166	0.82[EUR][1000 genomes]
rs10890327	0.85[EUR][1000 genomes]
rs10890330	0.86[CEU][hapmap]
rs11211101	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11211108	0.86[EUR][1000 genomes]
rs11211111	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.81[EUR][1000 genomes]
rs11211117	0.82[EUR][1000 genomes]
rs11211118	0.82[EUR][1000 genomes]
rs12037201	0.83[EUR][1000 genomes]
rs12037411	0.91[EUR][1000 genomes]
rs12046816	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs12097497	0.85[EUR][1000 genomes]
rs12139364	0.87[JPT][hapmap]
rs12410493	0.83[EUR][1000 genomes]
rs1417578	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1494812	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs1538969	0.81[EUR][1000 genomes]
rs1538970	0.83[EUR][1000 genomes]
rs17395553	0.91[EUR][1000 genomes]
rs1771551	0.88[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1826691	0.91[CEU][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.85[EUR][1000 genomes]
rs2050884	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2055145	0.86[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap]
rs2088100	0.85[EUR][1000 genomes]
rs2153607	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs2153609	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2185549	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2298018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs2487442	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2492836	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2492840	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28555082	0.82[EUR][1000 genomes]
rs3219463	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3219472	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3219489	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3790582	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.85[EUR][1000 genomes]
rs4520450	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs4660301	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660849	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4660852	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4660853	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4660854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4660855	0.83[EUR][1000 genomes]
rs4660858	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.82[EUR][1000 genomes]
rs61788261	0.84[EUR][1000 genomes]
rs61788281	0.82[EUR][1000 genomes]
rs61791362	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61791368	0.83[EUR][1000 genomes]
rs61791369	0.86[EUR][1000 genomes]
rs6657284	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap]
rs72686460	0.81[EUR][1000 genomes]
rs7417107	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7525849	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7528573	0.82[EUR][1000 genomes]
rs7531253	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.86[EUR][1000 genomes]
rs7532762	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7536135	0.85[EUR][1000 genomes]
rs7543428	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7544178	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7553318	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs781226	0.94[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs781230	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs781232	0.89[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs884962	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9326141	1.00[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9429072	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9429073	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9429074	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9429076	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9429158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9429159	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9429160	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9429161	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2153608	IPP	cis	lymphoblastoid	seeQTL
rs2153608	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs2153608	ST3GAL3	cis	parietal	SCAN
rs2153608	MUTYH	cis	multi-tissue	Pritchard
rs2153608	MAST2	cis	cerebellum	SCAN
rs2153608	SPATA19	trans	parietal	SCAN
rs2153608	TESK2	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45806600-45821600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:45807200-45814200	Weak transcription	Fetal Brain Male	brain
3	chr1:45807200-45825800	Weak transcription	Small Intestine	intestine
4	chr1:45808200-45814000	Weak transcription	Stomach Mucosa	stomach
5	chr1:45808800-45825600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:45809200-45815000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:45810000-45819800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:45810600-45814000	Weak transcription	Pancreas	Pancrea
9	chr1:45810600-45814600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:45810600-45825600	Weak transcription	Fetal Kidney	kidney
11	chr1:45810800-45820800	Weak transcription	HUVEC	blood vessel
12	chr1:45811000-45814000	Weak transcription	Aorta	Aorta
13	chr1:45811000-45814200	Weak transcription	Adipose Nuclei	Adipose
14	chr1:45811200-45814000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:45811200-45814000	Weak transcription	Brain Germinal Matrix	brain
16	chr1:45811200-45820800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:45811200-45825600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:45811200-45825600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:45811200-45825600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:45811400-45817000	Weak transcription	HepG2	liver
21	chr1:45811400-45825800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:45811400-45825800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:45811600-45825800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:45811800-45814600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:45812000-45815200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:45812000-45826000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:45812200-45814000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:45812200-45817200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:45812200-45825800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:45812400-45814000	Weak transcription	Dnd41	blood
31	chr1:45812400-45814200	Weak transcription	K562	blood
32	chr1:45812400-45814400	Weak transcription	Fetal Thymus	thymus
33	chr1:45812400-45815000	Weak transcription	GM12878-XiMat	blood
34	chr1:45812400-45816200	Enhancers	Placenta	Placenta
35	chr1:45812400-45820600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:45812400-45821200	Weak transcription	Primary T cells from cord blood	blood
37	chr1:45812400-45825600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr1:45812400-45825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:45812600-45814000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:45812600-45814200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:45812600-45816200	Enhancers	Hela-S3	cervix
42	chr1:45812600-45816800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:45812600-45817000	Weak transcription	Primary B cells from cord blood	blood
44	chr1:45812600-45817000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr1:45812600-45817800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:45812600-45819200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr1:45812600-45819600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:45812600-45825600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:45812600-45825800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:45812600-45825800	Weak transcription	Primary hematopoietic stem cells	blood

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