Variant report

Variant	rs16841283
Chromosome Location	chr4:7793671-7793672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7793303..7795239-chr4:7800745..7802759,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10516188	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10937859	0.82[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1106248	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs12501415	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12505487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12509628	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12511332	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12511919	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12512093	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12512166	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16841110	0.82[CEU][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes]
rs16841121	0.82[CEU][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16841150	0.82[CEU][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16841183	0.91[CEU][hapmap];0.92[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16841209	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16841268	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16841288	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2269877	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2285763	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2285768	0.87[AMR][1000 genomes]
rs34002186	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074746	0.88[YRI][hapmap]
rs4689168	1.00[YRI][hapmap]
rs56177309	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6824231	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6835308	0.90[CHB][hapmap]
rs730420	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73797315	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs877707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9683902	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9790400	0.82[CEU][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9790478	0.82[CEU][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats 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	8 gene(s)	inside rSNPs	diseases
5	nsv1006642	chr4:7786980-7811291	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7758400-7795400	Weak transcription	Hela-S3	cervix
2	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
3	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:7776400-7799000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:7776400-7800000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:7780200-7794400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:7780600-7800200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:7781000-7800000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:7781200-7796000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:7781400-7800400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:7781400-7801000	Weak transcription	Brain Substantia Nigra	brain
13	chr4:7781400-7801200	Weak transcription	Brain Anterior Caudate	brain
14	chr4:7781600-7807400	Weak transcription	Brain Angular Gyrus	brain
15	chr4:7783400-7794000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr4:7783400-7798800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:7783400-7799200	Weak transcription	HepG2	liver
18	chr4:7783800-7806200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr4:7784000-7794200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:7784000-7794400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:7784000-7801800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
23	chr4:7784200-7797800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:7784200-7800600	Weak transcription	Brain Hippocampus Middle	brain
25	chr4:7784200-7800600	Weak transcription	Esophagus	oesophagus
26	chr4:7784200-7802200	Weak transcription	Aorta	Aorta
27	chr4:7784200-7802800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr4:7784400-7794000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:7784800-7803400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:7785200-7796200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:7785800-7795800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr4:7785800-7803800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:7786000-7793800	Weak transcription	Fetal Heart	heart
34	chr4:7786000-7800800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr4:7786800-7795200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:7787000-7829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr4:7787200-7799000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr4:7787400-7800200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr4:7789200-7806600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:7789400-7799000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr4:7790200-7794400	Weak transcription	Brain Germinal Matrix	brain
42	chr4:7790400-7794400	Weak transcription	Colonic Mucosa	Colon
43	chr4:7790600-7795000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:7790800-7800800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:7790800-7803600	Strong transcription	HSMM	muscle
46	chr4:7791000-7801400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:7791000-7806600	Weak transcription	Psoas Muscle	Psoas
48	chr4:7791000-7829400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr4:7791200-7796400	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr4:7791200-7800800	Weak transcription	Spleen	Spleen

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