Variant report

Variant	rs6780250
Chromosome Location	chr3:142179497-142179498
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	chr3:142179124-142180279	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142167068..142168704-chr3:142178358..142179911,2	K562	blood:

Variant related genes	Relation type
ATR	TF binding region

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10935461	0.86[CHB][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs10935465	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1129393	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11925693	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12695761	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13061823	0.91[CHB][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13065075	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13067795	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13075471	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13085998	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13093869	0.82[EUR][1000 genomes]
rs13098343	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1357530	0.86[CEU][hapmap]
rs16852278	1.00[YRI][hapmap]
rs16852292	1.00[YRI][hapmap]
rs1983434	0.88[CEU][hapmap]
rs2030613	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs2049325	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs2140432	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs2227928	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2227930	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2862743	0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2862744	0.81[EUR][1000 genomes]
rs2862745	0.91[CHB][hapmap]
rs28708455	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3816805	0.86[CHB][hapmap];0.81[AMR][1000 genomes]
rs3922730	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4273389	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4413348	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs4441672	0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4597728	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57177110	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6440078	0.91[CHB][hapmap]
rs6440082	0.91[CHB][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6440086	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6440087	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6440088	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6440089	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6440090	0.83[EUR][1000 genomes]
rs6440091	0.81[EUR][1000 genomes]
rs6440092	0.83[EUR][1000 genomes]
rs6440093	0.83[EUR][1000 genomes]
rs6440094	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs6440098	0.88[CEU][hapmap]
rs6768093	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6769786	0.91[CHB][hapmap]
rs6770155	0.83[EUR][1000 genomes]
rs6772400	0.91[CHB][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6775583	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6775718	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6775813	0.86[CEU][hapmap]
rs6777255	0.81[ASN][1000 genomes]
rs6782400	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6785675	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6791816	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6792259	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6799752	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6800695	0.91[CHB][hapmap]
rs6802631	0.87[CHB][hapmap]
rs7610557	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs7615316	0.86[CEU][hapmap]
rs7623524	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7627694	0.80[EUR][1000 genomes]
rs7630130	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7631313	0.86[CEU][hapmap]
rs7634158	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7641330	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7646701	0.83[AMR][1000 genomes]
rs7647573	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7651071	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7652687	0.83[EUR][1000 genomes]
rs9289647	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs9289648	0.91[CHB][hapmap]
rs9683085	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9808914	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9808943	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9816736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820770	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821271	0.90[CHB][hapmap]
rs9825207	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9826786	0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9828178	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843148	0.87[CHB][hapmap]
rs9846960	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9847364	0.91[CHB][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9855140	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9855919	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9861997	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs9862919	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs9866958	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs9869842	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9871402	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9876254	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9879995	0.85[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:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142167200-142187600	Weak transcription	Esophagus	oesophagus
2	chr3:142167200-142192400	Weak transcription	Pancreas	Pancrea
3	chr3:142167400-142179600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:142167400-142199400	Weak transcription	Colonic Mucosa	Colon
5	chr3:142167400-142199600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:142167400-142234600	Weak transcription	Psoas Muscle	Psoas
7	chr3:142167600-142180000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:142167600-142180000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:142167600-142187200	Weak transcription	Fetal Brain Male	brain
10	chr3:142167600-142191800	Weak transcription	Fetal Brain Female	brain
11	chr3:142167600-142199600	Weak transcription	Ovary	ovary
12	chr3:142167600-142200000	Weak transcription	HSMMtube	muscle
13	chr3:142167600-142203000	Weak transcription	Brain Angular Gyrus	brain
14	chr3:142167800-142179800	Weak transcription	Brain Substantia Nigra	brain
15	chr3:142167800-142180000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:142167800-142180200	Weak transcription	HepG2	liver
17	chr3:142167800-142184800	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:142167800-142186400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:142167800-142188800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:142167800-142190400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:142167800-142199400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:142167800-142200000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr3:142167800-142200000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:142168000-142182600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:142168000-142192000	Weak transcription	Fetal Lung	lung
26	chr3:142168000-142200000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr3:142168000-142200000	Weak transcription	Fetal Kidney	kidney
28	chr3:142168200-142185800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:142168400-142180600	Strong transcription	Dnd41	blood
30	chr3:142168400-142186400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:142169000-142187000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:142169800-142192200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:142170200-142189200	Weak transcription	Aorta	Aorta
34	chr3:142170600-142199200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:142170600-142199600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:142170600-142203200	Weak transcription	Spleen	Spleen
37	chr3:142170800-142183200	Weak transcription	GM12878-XiMat	blood
38	chr3:142172400-142187600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:142172800-142199200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:142174000-142181400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:142174200-142180600	Strong transcription	A549	lung
42	chr3:142174400-142182600	Strong transcription	Primary B cells from cord blood	blood
43	chr3:142174400-142184000	Weak transcription	Osteobl	bone
44	chr3:142174800-142179800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:142174800-142183600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:142174800-142186400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr3:142175000-142180800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:142175400-142181000	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:142175400-142182000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:142175400-142184200	Weak transcription	Lung	lung

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