Variant report

Variant	rs13375787
Chromosome Location	chr1:75178713-75178714
allele	C/T
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	EP300	chr1:75178420-75178781	T-47D	breast:	n/a	n/a
2	FOXA1	chr1:75178589-75178848	T-47D	breast:	n/a	n/a
3	FOXA1	chr1:75178391-75178825	T-47D	breast:	n/a	n/a
4	GATA3	chr1:75178419-75178875	T-47D	breast:	n/a	n/a
5	GATA3	chr1:75178420-75178793	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:75176716..75178804-chr1:75183304..75185593,2	K562	blood:
2	chr1:75178320..75181136-chr1:75198418..75199986,2	MCF-7	breast:

Variant related genes	Relation type
CRYZ	TF binding region
ENSG00000162623	Chromatin interaction
ENSG00000116791	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11162945	0.81[CHB][hapmap]
rs1122338	0.82[AMR][1000 genomes]
rs1133891	0.85[CHB][hapmap];0.88[MEX][hapmap]
rs11485264	0.85[CHB][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes]
rs11487952	0.85[CHB][hapmap]
rs1581870	0.81[AMR][1000 genomes]
rs2032969	0.88[MEX][hapmap]
rs28436025	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28563168	0.82[AMR][1000 genomes]
rs28575168	0.82[AMR][1000 genomes]
rs28719150	0.83[AMR][1000 genomes]
rs28804147	0.82[AMR][1000 genomes]
rs28810187	0.82[AMR][1000 genomes]
rs3806161	0.82[AMR][1000 genomes]
rs3819947	0.85[CHB][hapmap]
rs4650004	0.85[CHB][hapmap]
rs4650005	1.00[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4650007	0.81[AMR][1000 genomes]
rs4650287	0.82[AMR][1000 genomes]
rs4650288	0.80[AMR][1000 genomes]
rs60292279	0.82[AMR][1000 genomes]
rs6681874	0.81[AMR][1000 genomes]
rs67696801	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs745108	0.85[CHB][hapmap];0.83[AMR][1000 genomes]
rs7540514	0.85[CHB][hapmap]
rs768223	0.82[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	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv830259	chr1:75089177-75241062	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv871152	chr1:75152186-75197533	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
5	esv1851105	chr1:75152186-75302921	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13375787	CRYZ	cis	lymphoblastoid	seeQTL
rs13375787	TYW3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75141800-75179600	Weak transcription	Aorta	Aorta
2	chr1:75156000-75183400	Weak transcription	Fetal Heart	heart
3	chr1:75159400-75187400	Weak transcription	NHEK	skin
4	chr1:75166200-75183800	Weak transcription	Brain Anterior Caudate	brain
5	chr1:75166400-75191400	Weak transcription	Placenta	Placenta
6	chr1:75166600-75182800	Weak transcription	HSMM	muscle
7	chr1:75166600-75194800	Weak transcription	Esophagus	oesophagus
8	chr1:75166800-75189200	Weak transcription	Spleen	Spleen
9	chr1:75167000-75181000	Weak transcription	Lung	lung
10	chr1:75167000-75197200	Weak transcription	Right Ventricle	heart
11	chr1:75167400-75181800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:75167600-75190600	Strong transcription	Liver	Liver
13	chr1:75167600-75190800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:75167800-75179600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:75167800-75190000	Strong transcription	Adipose Nuclei	Adipose
16	chr1:75168600-75181200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:75168600-75187000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:75168800-75186400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:75169000-75182200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:75169000-75189600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:75169400-75182800	Weak transcription	HUVEC	blood vessel
22	chr1:75169400-75190600	Strong transcription	Primary B cells from cord blood	blood
23	chr1:75169400-75191600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:75169600-75184600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:75169800-75191800	Weak transcription	Colonic Mucosa	Colon
26	chr1:75170000-75183600	Weak transcription	Fetal Kidney	kidney
27	chr1:75170400-75189600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:75170600-75179400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:75170600-75181800	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:75170600-75184400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:75170600-75184600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr1:75170600-75187000	Weak transcription	Stomach Mucosa	stomach
33	chr1:75170600-75187200	Weak transcription	Small Intestine	intestine
34	chr1:75170800-75187200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:75171000-75197200	Weak transcription	Brain Angular Gyrus	brain
36	chr1:75171200-75180400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:75171800-75189800	Strong transcription	HepG2	liver
38	chr1:75172000-75189400	Strong transcription	Fetal Muscle Leg	muscle
39	chr1:75172200-75178800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:75172200-75178800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:75172600-75182000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:75172600-75183200	Weak transcription	Dnd41	blood
43	chr1:75172600-75185600	Weak transcription	Fetal Thymus	thymus
44	chr1:75172600-75185800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:75172800-75179000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:75172800-75184200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:75173000-75179600	Weak transcription	NHDF-Ad	bronchial
48	chr1:75173200-75182400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:75173400-75189200	Strong transcription	Ovary	ovary
50	chr1:75173400-75189600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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