Variant report

Variant	rs4256152
Chromosome Location	chr3:142219542-142219543
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	GATA3	chr3:142219484-142220617	MCF-7	breast:	n/a	chr3:142219757-142219764 chr3:142220141-142220152
2	TCF7L2	chr3:142219527-142220585	PANC-1	pancreas:	n/a	n/a
3	GATA3	chr3:142219162-142220690	SK-N-SH	brain:	n/a	chr3:142219757-142219764 chr3:142220141-142220152
4	GATA3	chr3:142219454-142220636	SK-N-SH	brain:	n/a	chr3:142219757-142219764 chr3:142220141-142220152

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142219298..142222317-chr3:142296108..142299028,3	MCF-7	breast:
2	chr3:142217843..142219879-chr3:142296547..142298953,2	MCF-7	breast:

Variant related genes	Relation type
ATR	TF binding region
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10935460	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap]
rs10935463	0.89[EUR][1000 genomes]
rs1129391	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11708470	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11715514	0.90[EUR][1000 genomes]
rs11718899	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11916455	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11923612	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12629001	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12629713	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12634255	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12638158	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12639363	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13063075	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13065800	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13066441	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13068397	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13070239	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13071750	0.85[CEU][hapmap]
rs13072346	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13072355	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13075259	0.89[EUR][1000 genomes]
rs13082648	0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap]
rs13085247	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13085261	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13089219	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13092234	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13092593	0.93[EUR][1000 genomes]
rs13093304	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13099184	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs1485393	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap]
rs16852267	0.81[CHB][hapmap]
rs2227929	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2227931	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2306699	0.95[CHB][hapmap]
rs34392719	0.85[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap]
rs3762799	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap]
rs3923464	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4558780	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4582075	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes]
rs4683427	0.81[TSI][hapmap]
rs6440085	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6776402	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6786320	0.94[CHB][hapmap]
rs6809448	0.85[GIH][hapmap]
rs7432464	0.81[ASN][1000 genomes]
rs7623785	0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap]
rs7630115	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7636909	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7641914	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7643377	0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap]
rs7647329	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap]
rs953135	0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap]
rs9814159	0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap]
rs9829125	0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap]
rs9859834	0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap]
rs9867210	0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv528954	chr3:142164017-142219542	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv933680	chr3:142211643-142287189	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4256152	TRPC1	cis	parietal	SCAN
rs4256152	XRN1	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142167400-142234600	Weak transcription	Psoas Muscle	Psoas
2	chr3:142200000-142223200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:142200400-142243800	Weak transcription	Fetal Heart	heart
4	chr3:142200600-142271800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:142200800-142219800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:142201000-142239600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:142201000-142240600	Weak transcription	Fetal Brain Male	brain
8	chr3:142201200-142226800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:142201600-142273200	Weak transcription	Esophagus	oesophagus
10	chr3:142201800-142240600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:142201800-142243600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:142201800-142273800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:142202000-142221200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr3:142202000-142223800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:142202000-142231000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:142202000-142235200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr3:142202000-142239600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:142202200-142240200	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:142203000-142255200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:142203800-142223000	Weak transcription	Lung	lung
21	chr3:142203800-142225400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:142203800-142255200	Weak transcription	Gastric	stomach
23	chr3:142204200-142228000	Weak transcription	Pancreas	Pancrea
24	chr3:142204200-142253000	Weak transcription	Brain Substantia Nigra	brain
25	chr3:142204200-142273200	Weak transcription	Spleen	Spleen
26	chr3:142204200-142281400	Weak transcription	Colonic Mucosa	Colon
27	chr3:142207400-142238600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:142208200-142226600	Strong transcription	Primary B cells from cord blood	blood
29	chr3:142208400-142231000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:142208800-142239600	Weak transcription	Fetal Brain Female	brain
31	chr3:142209000-142225600	Weak transcription	Brain Angular Gyrus	brain
32	chr3:142209400-142271800	Weak transcription	HepG2	liver
33	chr3:142210400-142225000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:142210400-142231000	Weak transcription	Aorta	Aorta
35	chr3:142210400-142240600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:142211200-142223800	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:142211400-142221600	Weak transcription	Small Intestine	intestine
38	chr3:142211400-142222400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:142211400-142226000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:142211400-142240600	Weak transcription	Brain Germinal Matrix	brain
41	chr3:142212000-142251400	Weak transcription	Brain Anterior Caudate	brain
42	chr3:142212200-142219800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:142212200-142221000	Weak transcription	Fetal Kidney	kidney
44	chr3:142212600-142225200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:142212600-142240000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:142212600-142240000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:142212800-142225200	Weak transcription	Thymus	Thymus
48	chr3:142212800-142238600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr3:142213200-142221000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:142213600-142219600	Weak transcription	HUVEC	blood vessel

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