Variant report

Variant	rs13075471
Chromosome Location	chr3:142191659-142191660
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	POLR2A	chr3:142191551-142191659	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142176585..142179002-chr3:142191298..142192825,2	K562	blood:
2	chr3:142164765..142166960-chr3:142189962..142191863,2	K562	blood:

Variant related genes	Relation type
ENSG00000244327	TF binding region
ATR	TF binding region
ENSG00000175054	Chromatin interaction
ENSG00000114127	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10935461	0.85[EUR][1000 genomes]
rs10935465	0.81[ASN][1000 genomes]
rs11925693	0.86[EUR][1000 genomes]
rs12695761	0.89[EUR][1000 genomes]
rs13061823	0.89[EUR][1000 genomes]
rs13065075	0.81[ASN][1000 genomes]
rs13067795	0.81[ASN][1000 genomes]
rs13069307	0.83[EUR][1000 genomes]
rs13085998	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13098343	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2086933	0.85[EUR][1000 genomes]
rs2227930	0.81[ASN][1000 genomes]
rs2862743	0.86[EUR][1000 genomes]
rs2862744	0.87[EUR][1000 genomes]
rs2862745	0.84[EUR][1000 genomes]
rs2862746	0.85[EUR][1000 genomes]
rs28708455	0.89[EUR][1000 genomes]
rs3816805	0.84[EUR][1000 genomes]
rs3922730	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4273389	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4434160	0.81[EUR][1000 genomes]
rs4441672	0.89[EUR][1000 genomes]
rs4597728	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4608715	0.85[EUR][1000 genomes]
rs57177110	0.89[EUR][1000 genomes]
rs6414350	0.83[EUR][1000 genomes]
rs6440077	0.81[EUR][1000 genomes]
rs6440078	0.82[EUR][1000 genomes]
rs6440082	0.87[EUR][1000 genomes]
rs6440087	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6769786	0.85[EUR][1000 genomes]
rs6772400	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6775583	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6775718	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6777255	0.82[EUR][1000 genomes]
rs6780250	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6782897	0.81[EUR][1000 genomes]
rs6785675	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6791816	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6800695	0.85[EUR][1000 genomes]
rs6802631	0.84[EUR][1000 genomes]
rs7613664	0.84[EUR][1000 genomes]
rs7623524	0.83[EUR][1000 genomes]
rs7627694	0.86[EUR][1000 genomes]
rs7630130	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7634158	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7641330	0.85[EUR][1000 genomes]
rs7646701	0.83[EUR][1000 genomes]
rs7647573	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7651071	0.84[EUR][1000 genomes]
rs7652687	0.89[EUR][1000 genomes]
rs9289647	0.84[EUR][1000 genomes]
rs9289648	0.85[EUR][1000 genomes]
rs9683085	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9808914	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9808943	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9816736	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9820770	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9821271	0.84[EUR][1000 genomes]
rs9826786	0.89[EUR][1000 genomes]
rs9828178	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9846960	0.86[EUR][1000 genomes]
rs9847364	0.89[EUR][1000 genomes]
rs9855140	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9855919	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9861997	0.85[EUR][1000 genomes]
rs9869842	0.81[ASN][1000 genomes]
rs9876254	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142167200-142192400	Weak transcription	Pancreas	Pancrea
2	chr3:142167400-142199400	Weak transcription	Colonic Mucosa	Colon
3	chr3:142167400-142199600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:142167400-142234600	Weak transcription	Psoas Muscle	Psoas
5	chr3:142167600-142191800	Weak transcription	Fetal Brain Female	brain
6	chr3:142167600-142199600	Weak transcription	Ovary	ovary
7	chr3:142167600-142200000	Weak transcription	HSMMtube	muscle
8	chr3:142167600-142203000	Weak transcription	Brain Angular Gyrus	brain
9	chr3:142167800-142199400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:142167800-142200000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:142167800-142200000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:142168000-142192000	Weak transcription	Fetal Lung	lung
13	chr3:142168000-142200000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:142168000-142200000	Weak transcription	Fetal Kidney	kidney
15	chr3:142169800-142192200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:142170600-142199200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:142170600-142199600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:142170600-142203200	Weak transcription	Spleen	Spleen
19	chr3:142172800-142199200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:142175400-142192000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:142175400-142192400	Weak transcription	Fetal Stomach	stomach
22	chr3:142175400-142199200	Weak transcription	Thymus	Thymus
23	chr3:142176200-142199200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:142177400-142199200	Weak transcription	Right Ventricle	heart
25	chr3:142177600-142200200	Weak transcription	Hela-S3	cervix
26	chr3:142177800-142199200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:142177800-142200000	Weak transcription	NH-A	brain
28	chr3:142178000-142191800	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:142178000-142199200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:142178000-142199600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:142178000-142200000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:142178200-142192000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:142178200-142192000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:142178200-142192000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:142178200-142199200	Weak transcription	Placenta	Placenta
36	chr3:142178200-142199400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:142178200-142199600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:142178200-142200000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr3:142178400-142192000	Weak transcription	Fetal Thymus	thymus
40	chr3:142178400-142199600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:142178400-142200000	Weak transcription	HMEC	breast
42	chr3:142178400-142200200	Weak transcription	Fetal Heart	heart
43	chr3:142178600-142191800	Weak transcription	Fetal Muscle Leg	muscle
44	chr3:142178600-142199200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:142178600-142199200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:142178600-142200200	Weak transcription	NHDF-Ad	bronchial
47	chr3:142178600-142200200	Weak transcription	NHEK	skin
48	chr3:142178800-142200000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:142178800-142200000	Weak transcription	K562	blood
50	chr3:142179400-142199400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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