Variant report

Variant	rs1879420
Chromosome Location	chr3:150466564-150466565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:150454729..150455798-chr3:150465746..150466877,4	MCF-7	breast:
2	chr3:150465849..150466597-chr3:150480619..150481165,2	MCF-7	breast:
3	chr3:150320747..150322493-chr3:150463869..150466660,3	MCF-7	breast:
4	chr3:150457190..150462784-chr3:150464439..150467778,5	K562	blood:
5	chr3:150455149..150455742-chr3:150465878..150466660,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120742	Chromatin interaction
ENSG00000181788	Chromatin interaction
ENSG00000198843	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10513377	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs1444197	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs1533711	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs16862837	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs16862842	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1838337	0.83[AMR][1000 genomes]
rs1879421	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1879422	0.82[ASN][1000 genomes]
rs1915365	0.83[AMR][1000 genomes]
rs1991781	0.82[ASN][1000 genomes]
rs2014279	1.00[CEU][hapmap]
rs2018246	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs2116684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2120596	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34348847	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs3851356	1.00[CEU][hapmap]
rs41372346	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes]
rs41454348	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs481236	0.81[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs502941	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs55899470	0.82[ASN][1000 genomes]
rs56725170	0.82[ASN][1000 genomes]
rs57275328	0.81[ASN][1000 genomes]
rs57359526	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57824095	0.82[ASN][1000 genomes]
rs57965761	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58418105	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs594926	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs60092981	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60523415	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs60538652	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61628582	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440697	1.00[CEU][hapmap]
rs6788895	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6789306	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6805481	1.00[CEU][hapmap]
rs73006998	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73006999	0.82[ASN][1000 genomes]
rs73008903	0.82[ASN][1000 genomes]
rs73008905	0.82[ASN][1000 genomes]
rs73008907	0.82[ASN][1000 genomes]
rs73010930	0.82[ASN][1000 genomes]
rs73010947	0.81[ASN][1000 genomes]
rs7615125	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7615292	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7617507	1.00[CEU][hapmap]
rs7628481	1.00[CEU][hapmap]
rs7628776	1.00[CEU][hapmap]
rs7636866	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs939476	0.95[CHB][hapmap];0.85[CHD][hapmap];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150453800-150478000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:150454600-150469800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:150454600-150477200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:150454800-150467200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:150456400-150477600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:150456600-150477600	Weak transcription	Fetal Brain Male	brain
7	chr3:150456800-150477400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:150457000-150478800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:150457600-150477600	Weak transcription	HUVEC	blood vessel
10	chr3:150458200-150469600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:150458400-150471600	Genic enhancers	HepG2	liver
12	chr3:150458600-150467400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:150458800-150469400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:150459000-150477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:150459400-150468400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
16	chr3:150460200-150477600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:150460400-150467800	Enhancers	Liver	Liver
18	chr3:150460400-150468800	Weak transcription	Colonic Mucosa	Colon
19	chr3:150460400-150469000	Weak transcription	Fetal Thymus	thymus
20	chr3:150460400-150469600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:150460400-150475200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:150460400-150477600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:150460600-150469600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:150460600-150469800	Weak transcription	Fetal Stomach	stomach
25	chr3:150460600-150470600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:150460600-150470800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:150461200-150471800	Enhancers	Stomach Mucosa	stomach
28	chr3:150461200-150474000	Weak transcription	Dnd41	blood
29	chr3:150461600-150468200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:150461600-150469000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:150461600-150469200	Weak transcription	Primary T cells from cord blood	blood
32	chr3:150461800-150468600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:150461800-150469600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:150461800-150472000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:150462800-150477000	Weak transcription	Brain Angular Gyrus	brain
36	chr3:150463000-150475400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:150463000-150477800	Weak transcription	NH-A	brain
38	chr3:150463000-150478400	Weak transcription	HSMM	muscle
39	chr3:150463200-150467800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:150463200-150468400	Weak transcription	Fetal Lung	lung
41	chr3:150463200-150469600	Weak transcription	Fetal Muscle Leg	muscle
42	chr3:150463200-150469600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:150463200-150469600	Weak transcription	HMEC	breast
44	chr3:150463200-150470600	Weak transcription	NHLF	lung
45	chr3:150463200-150475600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:150463200-150477600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:150463400-150468400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr3:150463600-150467400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:150463800-150469000	Enhancers	Ovary	ovary
50	chr3:150464200-150466800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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