Variant report

Variant	rs2363641
Chromosome Location	chr14:77783134-77783135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr14:77783020-77783170	GM12873	blood:	n/a	n/a
2	CTCF	chr14:77783100-77783250	HVMF	connective:	n/a	n/a
3	FOS	chr14:77783124-77783356	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr14:77781065..77784774-chr14:77784883..77788972,8	K562	blood:
2	chr14:77782973..77788435-chr14:78081530..78084931,5	MCF-7	breast:
3	chr14:77782277..77784814-chr14:77790123..77792758,2	K562	blood:
4	chr14:77747430..77750741-chr14:77781891..77784413,3	MCF-7	breast:
5	chr14:77782500..77784938-chr14:77842054..77844042,2	MCF-7	breast:
6	chr14:77603673..77605750-chr14:77781536..77783991,2	MCF-7	breast:
7	chr14:77559718..77567556-chr14:77781210..77790475,16	MCF-7	breast:
8	chr14:77781658..77784050-chr14:77784883..77787153,4	K562	blood:
9	chr14:77766725..77768587-chr14:77781835..77783653,26	MCF-7	breast:

No data

Variant related genes	Relation type
POMT2	TF binding region
GSTZ1	TF binding region
ENSG00000198894	Chromatin interaction
ENSG00000100596	Chromatin interaction
ENSG00000259164	Chromatin interaction
ENSG00000100577	Chromatin interaction
ENSG00000100580	Chromatin interaction
ENSG00000100583	Chromatin interaction
ENSG00000009830	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10138030	0.87[JPT][hapmap]
rs11547793	0.91[JPT][hapmap]
rs11624564	0.86[CHB][hapmap]
rs11624859	0.88[ASN][1000 genomes]
rs11626281	0.86[ASN][1000 genomes]
rs11627257	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs12431465	0.80[ASN][1000 genomes]
rs17105672	1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2042045	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2098380	0.82[CHB][hapmap]
rs2111699	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2193594	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2216089	0.86[CHB][hapmap]
rs2270421	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2270423	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs2287387	0.95[CHB][hapmap]
rs2287388	0.91[JPT][hapmap]
rs2287392	0.91[JPT][hapmap]
rs2287395	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs2363642	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2363643	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2885854	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759733	0.88[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3783986	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs3783988	0.91[JPT][hapmap]
rs3783989	0.91[JPT][hapmap]
rs3815626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147578	0.94[CHB][hapmap];0.81[EUR][1000 genomes]
rs4147579	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4899650	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4903567	0.95[CHB][hapmap]
rs4903569	0.91[ASN][1000 genomes]
rs59630055	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61990299	0.88[ASN][1000 genomes]
rs6574367	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];0.94[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]
rs6574368	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67873774	0.88[ASN][1000 genomes]
rs7142812	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7158951	0.86[CHB][hapmap]
rs7159558	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs7160188	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7160195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975	0.89[EUR][1000 genomes]
rs8007615	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8008449	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8009261	0.86[CHB][hapmap]
rs8009733	0.86[CHB][hapmap]
rs8016187	0.90[CEU][hapmap];0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431017	chr14:76938089-77854647	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription 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	107 gene(s)	inside rSNPs	diseases
2	nsv902105	chr14:77764884-77801431	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv902106	chr14:77767978-77801431	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2363641	GSTZ1	cis	lymphoblastoid	seeQTL
rs2363641	NPC2	cis	parietal	SCAN
rs2363641	AHSA1	cis	cerebellum	SCAN
rs2363641	GSTZ1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77751400-77786200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr14:77770800-77785800	Weak transcription	K562	blood
3	chr14:77772600-77783800	Weak transcription	Dnd41	blood
4	chr14:77772600-77785800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr14:77772600-77786400	Weak transcription	Aorta	Aorta
6	chr14:77772800-77785800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr14:77773800-77786800	Weak transcription	Small Intestine	intestine
8	chr14:77774000-77783400	Weak transcription	Stomach Mucosa	stomach
9	chr14:77775800-77785600	Weak transcription	HUVEC	blood vessel
10	chr14:77775800-77786200	Weak transcription	Primary T cells from cord blood	blood
11	chr14:77776000-77786000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr14:77776000-77786400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr14:77776200-77786200	Weak transcription	Primary B cells from cord blood	blood
14	chr14:77776600-77785800	Weak transcription	Fetal Brain Male	brain
15	chr14:77777000-77784800	Weak transcription	Fetal Brain Female	brain
16	chr14:77777400-77785200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr14:77778000-77785800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr14:77778400-77784400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr14:77778800-77785800	Enhancers	Brain Cingulate Gyrus	brain
20	chr14:77779000-77785800	Enhancers	Brain Anterior Caudate	brain
21	chr14:77779000-77786200	Enhancers	Fetal Intestine Large	intestine
22	chr14:77779200-77783200	Enhancers	Brain Substantia Nigra	brain
23	chr14:77779200-77784600	Enhancers	HepG2	liver
24	chr14:77779200-77785400	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr14:77779200-77785800	Enhancers	Brain Angular Gyrus	brain
26	chr14:77779400-77783600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr14:77779400-77784200	Enhancers	Psoas Muscle	Psoas
28	chr14:77779400-77784600	Enhancers	Fetal Intestine Small	intestine
29	chr14:77779400-77785800	Enhancers	HMEC	breast
30	chr14:77779400-77786400	Enhancers	Fetal Muscle Leg	muscle
31	chr14:77779600-77785800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr14:77779800-77783400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr14:77780200-77783800	Enhancers	Adipose Nuclei	Adipose
34	chr14:77780400-77783600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr14:77780400-77784200	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr14:77780800-77783600	Enhancers	Fetal Muscle Trunk	muscle
37	chr14:77781000-77783200	Weak transcription	NH-A	brain
38	chr14:77781200-77783200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr14:77781200-77785600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr14:77781200-77785800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr14:77781200-77786000	Weak transcription	Osteobl	bone
42	chr14:77781200-77786400	Weak transcription	Esophagus	oesophagus
43	chr14:77781400-77783200	Genic enhancers	Fetal Stomach	stomach
44	chr14:77781400-77783200	Weak transcription	HSMM	muscle
45	chr14:77781600-77783200	Weak transcription	Lung	lung
46	chr14:77781600-77783800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr14:77781600-77786400	Weak transcription	Ovary	ovary
48	chr14:77781800-77783200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr14:77781800-77783200	Weak transcription	Gastric	stomach
50	chr14:77781800-77783400	Weak transcription	Brain Germinal Matrix	brain

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