Variant report

Variant	rs13140998
Chromosome Location	chr4:143641027-143641028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:143637297..143639595-chr4:143640905..143643324,3	MCF-7	breast:
2	chr4:143393131..143399799-chr4:143636317..143645681,15	MCF-7	breast:
3	chr4:143634044..143636846-chr4:143637396..143641073,3	MCF-7	breast:
4	chr4:143392644..143398601-chr4:143638137..143645320,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10023146	0.87[ASN][1000 genomes]
rs10034956	0.87[ASN][1000 genomes]
rs10049507	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11100756	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11725795	0.87[ASN][1000 genomes]
rs11732995	0.81[AFR][1000 genomes]
rs13103261	0.80[ASN][1000 genomes]
rs13105531	0.80[ASN][1000 genomes]
rs13108947	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112871	0.87[ASN][1000 genomes]
rs13115869	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13116732	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13133396	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13135210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1373033	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1373664	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1441412	0.80[ASN][1000 genomes]
rs1441416	0.87[ASN][1000 genomes]
rs1899564	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2322814	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28367408	0.80[ASN][1000 genomes]
rs28410519	0.80[ASN][1000 genomes]
rs28421948	0.80[ASN][1000 genomes]
rs28453834	0.80[ASN][1000 genomes]
rs28462985	0.80[ASN][1000 genomes]
rs28508323	0.87[ASN][1000 genomes]
rs28533753	0.80[ASN][1000 genomes]
rs28608029	0.87[ASN][1000 genomes]
rs28665985	0.80[ASN][1000 genomes]
rs28667040	0.80[ASN][1000 genomes]
rs28685292	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34032529	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34241470	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34412123	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34611963	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34804364	0.80[ASN][1000 genomes]
rs35053070	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35416729	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35838997	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35918867	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36042265	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62331921	0.80[ASN][1000 genomes]
rs62331922	0.80[ASN][1000 genomes]
rs62331933	0.80[ASN][1000 genomes]
rs62331934	0.80[ASN][1000 genomes]
rs7662067	0.80[ASN][1000 genomes]
rs986081	0.87[ASN][1000 genomes]
rs9994239	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9994268	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830101	chr4:143518810-143684392	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv595606	chr4:143631691-143729595	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv880174	chr4:143639498-143848024	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription 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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143620800-143642000	Weak transcription	Fetal Heart	heart
2	chr4:143625200-143641600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:143630800-143650200	Weak transcription	Aorta	Aorta
4	chr4:143635000-143648200	Weak transcription	Thymus	Thymus
5	chr4:143637200-143653000	Weak transcription	Left Ventricle	heart
6	chr4:143639200-143641800	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr4:143639600-143641400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:143639600-143641600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr4:143639600-143647000	Enhancers	Dnd41	blood
10	chr4:143640000-143641200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:143640000-143641400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr4:143640200-143641400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:143640200-143641800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:143640200-143642200	Enhancers	NHEK	skin
15	chr4:143640200-143642800	Enhancers	HMEC	breast
16	chr4:143640600-143641600	Enhancers	Primary hematopoietic stem cells	blood
17	chr4:143640800-143641400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:143641000-143641200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:143641000-143641200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:143641000-143641400	Enhancers	Primary T cells from cord blood	blood
21	chr4:143641000-143641400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr4:143641000-143641400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr4:143641000-143641400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:143641000-143641400	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr4:143641000-143641400	Enhancers	NHDF-Ad	bronchial
26	chr4:143641000-143641400	Enhancers	Osteobl	bone
27	chr4:143641000-143641800	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr4:143641000-143641800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr4:143641000-143642600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr4:143641000-143642600	Enhancers	NH-A	brain

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