Variant report

Variant	rs4915379
Chromosome Location	chr1:197161428-197161429
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:197160099..197163590-chr1:197167883..197170766,5	MCF-7	breast:
2	chr1:197148315..197153030-chr1:197158427..197161690,6	K562	blood:
3	chr1:197108980..197111975-chr1:197160260..197161833,2	K562	blood:

Variant related genes	Relation type
ENSG00000177888	Chromatin interaction
ENSG00000134376	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10429911	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10732295	1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10732296	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10754219	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10801593	1.00[EUR][1000 genomes]
rs10801594	1.00[EUR][1000 genomes]
rs1115247	0.87[CEU][hapmap]
rs12092294	0.87[CEU][hapmap];0.95[GIH][hapmap];0.92[MKK][hapmap]
rs12677	0.87[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap]
rs1332662	0.87[CEU][hapmap]
rs1332663	0.89[ASW][hapmap];0.87[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs1412631	0.87[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs1412632	0.89[ASW][hapmap];0.87[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs1412634	0.87[CEU][hapmap];0.86[YRI][hapmap]
rs1415217	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1556763	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1571964	0.87[CEU][hapmap];0.95[GIH][hapmap]
rs1764629	0.83[EUR][1000 genomes]
rs1764800	1.00[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs1888991	0.84[ASW][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs2026429	0.89[ASW][hapmap];0.87[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs2151134	1.00[CEU][hapmap]
rs4244141	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4342879	1.00[CEU][hapmap]
rs4350226	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs476390	1.00[CEU][hapmap]
rs4915337	0.87[CEU][hapmap]
rs4915345	0.85[AFR][1000 genomes]
rs4915378	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5029273	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs510135	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs518149	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs615647	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs616675	1.00[CEU][hapmap]
rs6428390	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6656448	1.00[CEU][hapmap]
rs6656858	0.89[ASW][hapmap];0.87[CEU][hapmap];0.95[GIH][hapmap]
rs6677082	0.87[CEU][hapmap];0.95[GIH][hapmap]
rs6701681	0.84[EUR][1000 genomes]
rs6703400	0.87[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs7513826	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7520503	1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7523013	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7534353	0.86[CEU][hapmap]
rs7542397	0.87[CEU][hapmap]
rs7554802	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7554890	1.00[EUR][1000 genomes]
rs7554995	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs877897	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv873070	chr1:197079671-197165014	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers 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 target site	6 gene(s)	inside rSNPs	diseases
6	nsv873071	chr1:197079671-197187605	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv873072	chr1:197079671-197221248	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv548871	chr1:197106604-197168233	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv873073	chr1:197107074-197221248	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv947366	chr1:197157398-197163669	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197116600-197169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:197125400-197168400	Weak transcription	Psoas Muscle	Psoas
3	chr1:197125600-197169600	Weak transcription	Esophagus	oesophagus
4	chr1:197126400-197169600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:197135200-197161800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:197136000-197161600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:197141400-197166200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:197143200-197165800	Weak transcription	Small Intestine	intestine
9	chr1:197149800-197165400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:197152400-197168600	Weak transcription	Stomach Mucosa	stomach
11	chr1:197152800-197161600	Strong transcription	HSMM	muscle
12	chr1:197153200-197165000	Weak transcription	Fetal Heart	heart
13	chr1:197154800-197163400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:197155400-197163600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:197156400-197164400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:197156600-197164000	Weak transcription	Hela-S3	cervix
17	chr1:197157200-197164000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:197157200-197165600	Weak transcription	Aorta	Aorta
19	chr1:197157200-197166800	Weak transcription	NHEK	skin
20	chr1:197157400-197162200	Weak transcription	Fetal Brain Male	brain
21	chr1:197157400-197162800	Weak transcription	Ovary	ovary
22	chr1:197157400-197164000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:197157400-197164000	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:197157400-197164000	Weak transcription	GM12878-XiMat	blood
25	chr1:197157400-197164200	Weak transcription	Brain Angular Gyrus	brain
26	chr1:197157400-197166800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:197157400-197166800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:197157400-197166800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:197157400-197166800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:197157400-197166800	Weak transcription	Right Ventricle	heart
31	chr1:197157400-197166800	Weak transcription	Thymus	Thymus
32	chr1:197157400-197166800	Weak transcription	HSMMtube	muscle
33	chr1:197157400-197166800	Weak transcription	NHLF	lung
34	chr1:197157400-197167000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:197157400-197168400	Weak transcription	Left Ventricle	heart
36	chr1:197157400-197169400	Weak transcription	Colonic Mucosa	Colon
37	chr1:197157400-197169600	Weak transcription	Pancreas	Pancrea
38	chr1:197157600-197162200	Weak transcription	K562	blood
39	chr1:197157600-197164000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr1:197157600-197165000	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:197157600-197165000	Weak transcription	Brain Substantia Nigra	brain
42	chr1:197157600-197167000	Weak transcription	HMEC	breast
43	chr1:197157600-197167000	Weak transcription	HUVEC	blood vessel
44	chr1:197157600-197167600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:197157800-197165600	Weak transcription	HepG2	liver
46	chr1:197158000-197164600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:197158200-197163400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:197158200-197165800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:197158400-197164400	Weak transcription	A549	lung
50	chr1:197158400-197165000	Weak transcription	Brain Cingulate Gyrus	brain

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