Variant report

Variant	rs6442042
Chromosome Location	chr3:46988654-46988655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:46942667..46944620-chr3:46986480..46988761,2	K562	blood:
2	chr3:46988617..46992704-chr3:46994196..46998366,6	K562	blood:
3	chr3:46986646..46988898-chr3:47016265..47017961,2	K562	blood:
4	chr3:46985961..46989571-chr3:47058662..47060411,3	K562	blood:
5	chr3:46988418..46991129-chr3:46992863..46994642,3	MCF-7	breast:
6	chr3:46984582..46987726-chr3:46988178..46990594,3	K562	blood:
7	chr3:46987488..46994423-chr3:47016253..47019914,6	MCF-7	breast:
8	chr3:46986886..46990722-chr3:47020544..47025137,5	MCF-7	breast:
9	chr3:46734374..46736416-chr3:46987784..46989611,2	MCF-7	breast:
10	chr3:46988383..46991103-chr3:47025292..47027507,2	MCF-7	breast:
11	chr3:46983747..46991522-chr3:47014474..47023916,13	MCF-7	breast:
12	chr3:46987136..46991583-chr3:47027983..47031367,6	K562	blood:
13	chr3:46968433..46974874-chr3:46985986..46991697,10	MCF-7	breast:
14	chr3:46987457..46990723-chr3:46999774..47002993,3	MCF-7	breast:
15	chr3:46983597..46986093-chr3:46988070..46989778,2	MCF-7	breast:
16	chr3:46988088..46989870-chr3:47001912..47004802,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160799	Chromatin interaction
ENSG00000160796	Chromatin interaction
ENSG00000178038	Chromatin interaction
ENSG00000160801	Chromatin interaction

Extended variants
information (count: 155 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10461017	0.84[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10461019	0.82[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs11130108	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130109	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11706212	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11708257	0.82[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709693	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709876	0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11713537	0.82[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs11928558	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12330516	1.00[EUR][1000 genomes]
rs12487763	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs13062185	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs13079416	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13082531	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13323092	1.00[EUR][1000 genomes]
rs1378818	0.84[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463394	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466272	0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466273	0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466274	0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs1473382	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473384	1.00[EUR][1000 genomes]
rs1473385	1.00[EUR][1000 genomes]
rs1563431	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1563432	1.00[EUR][1000 genomes]
rs1814564	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1869870	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2124509	0.84[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2124510	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs2385863	1.00[EUR][1000 genomes]
rs2385868	0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2385869	0.84[YRI][hapmap];0.89[AMR][1000 genomes]
rs2385872	0.90[AMR][1000 genomes]
rs28735306	1.00[EUR][1000 genomes]
rs2891887	0.89[AMR][1000 genomes]
rs2891893	0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs34147581	1.00[EUR][1000 genomes]
rs35366910	1.00[EUR][1000 genomes]
rs4018904	1.00[EUR][1000 genomes]
rs4282092	0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs4289375	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4324490	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4373094	0.84[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4378998	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4389512	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4450857	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4478107	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4522803	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4525902	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4543047	0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682828	1.00[EUR][1000 genomes]
rs4682832	0.95[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682833	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682834	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4682835	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682836	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682838	0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682841	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682843	0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682846	1.00[EUR][1000 genomes]
rs4682847	1.00[EUR][1000 genomes]
rs4683277	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683279	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683282	0.91[YRI][hapmap]
rs4683283	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683284	0.82[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683285	0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683286	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683288	1.00[EUR][1000 genomes]
rs4683289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683290	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683291	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683292	0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683293	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683303	1.00[EUR][1000 genomes]
rs6442041	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442043	0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442044	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442047	0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442048	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6766676	0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6768169	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6775797	1.00[EUR][1000 genomes]
rs6780994	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6785462	0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6804732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6806521	0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808052	1.00[EUR][1000 genomes]
rs6808117	1.00[EUR][1000 genomes]
rs6808629	1.00[EUR][1000 genomes]
rs6809904	0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621530	0.80[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7624549	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7625011	0.91[YRI][hapmap]
rs7630154	1.00[EUR][1000 genomes]
rs7630904	0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7638549	0.82[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7641494	1.00[EUR][1000 genomes]
rs7643868	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7644382	1.00[EUR][1000 genomes]
rs7646076	0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7649941	0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650142	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs936173	1.00[EUR][1000 genomes]
rs936177	0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936178	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936179	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936180	0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936181	0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936182	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936185	1.00[EUR][1000 genomes]
rs936186	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9637426	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9810881	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9812407	1.00[EUR][1000 genomes]
rs9819344	1.00[EUR][1000 genomes]
rs9819475	1.00[EUR][1000 genomes]
rs9823480	1.00[EUR][1000 genomes]
rs9826488	1.00[EUR][1000 genomes]
rs9827293	1.00[EUR][1000 genomes]
rs9828473	1.00[EUR][1000 genomes]
rs9833500	1.00[EUR][1000 genomes]
rs9836801	1.00[EUR][1000 genomes]
rs9850151	1.00[EUR][1000 genomes]
rs9852167	1.00[EUR][1000 genomes]
rs9861247	1.00[EUR][1000 genomes]
rs9861265	1.00[EUR][1000 genomes]
rs9862711	1.00[EUR][1000 genomes]
rs9869489	1.00[EUR][1000 genomes]
rs9878813	1.00[EUR][1000 genomes]
rs9883152	1.00[EUR][1000 genomes]
rs9883909	1.00[EUR][1000 genomes]
rs9990284	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1012682	chr3:46973552-47016357	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats 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	28 gene(s)	inside rSNPs	diseases
9	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46976200-46990200	Weak transcription	Fetal Brain Male	brain
2	chr3:46977000-47000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:46978000-46990600	Strong transcription	Fetal Stomach	stomach
4	chr3:46979400-46989200	Weak transcription	NHDF-Ad	bronchial
5	chr3:46979600-46994600	Genic enhancers	Fetal Thymus	thymus
6	chr3:46980200-46990800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:46982200-46989000	Weak transcription	HSMMtube	muscle
8	chr3:46982400-46989000	Weak transcription	Aorta	Aorta
9	chr3:46982600-46988800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:46982600-46988800	Weak transcription	NHLF	lung
11	chr3:46982600-46989000	Weak transcription	Brain Germinal Matrix	brain
12	chr3:46982800-46992600	Enhancers	Left Ventricle	heart
13	chr3:46983000-46989400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:46983000-46992600	Enhancers	Small Intestine	intestine
15	chr3:46983200-46989400	Enhancers	HMEC	breast
16	chr3:46983200-46989600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr3:46983200-46992400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr3:46983400-46991200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:46983600-46992600	Enhancers	Psoas Muscle	Psoas
20	chr3:46983600-46992600	Enhancers	Right Atrium	heart
21	chr3:46983600-46994000	Enhancers	HUVEC	blood vessel
22	chr3:46984000-46989200	Weak transcription	Fetal Brain Female	brain
23	chr3:46984000-46989400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:46984200-46989000	Genic enhancers	K562	blood
25	chr3:46984200-46996400	Enhancers	Liver	Liver
26	chr3:46984400-46989000	Enhancers	Esophagus	oesophagus
27	chr3:46984800-46989200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:46984800-46989400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr3:46985000-46988800	Enhancers	Colonic Mucosa	Colon
30	chr3:46985000-46989400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:46985000-46989800	Enhancers	Brain Substantia Nigra	brain
32	chr3:46985000-46992000	Enhancers	Pancreas	Pancrea
33	chr3:46985000-46992600	Enhancers	Right Ventricle	heart
34	chr3:46985200-46989000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr3:46985200-46991800	Genic enhancers	Fetal Intestine Small	intestine
36	chr3:46985600-46989000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr3:46985600-46995200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr3:46985800-46990000	Genic enhancers	Primary B cells from peripheral blood	blood
39	chr3:46985800-46990800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:46985800-46994200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:46985800-47004400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr3:46986000-46989000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr3:46986000-46990800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:46986000-46991000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr3:46986200-46989200	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr3:46986200-46989600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr3:46986200-46991000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:46986400-46991200	Enhancers	Placenta Amnion	Placenta Amnion
49	chr3:46986600-46988800	Weak transcription	Brain Anterior Caudate	brain
50	chr3:46986600-46990600	Genic enhancers	GM12878-XiMat	blood

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