Variant report

Variant	rs9489540
Chromosome Location	chr6:119237335-119237336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119236200..119239716-chr6:119244057..119245894,3	MCF-7	breast:
2	chr6:119215924..119218586-chr6:119236069..119238504,2	K562	blood:
3	chr6:119232668..119234760-chr6:119235529..119238210,3	K562	blood:
4	chr6:119237237..119239563-chr6:119244065..119246432,2	K562	blood:
5	chr6:119235128..119240237-chr6:119246100..119252076,6	K562	blood:
6	chr6:119235730..119238725-chr6:119250576..119253329,2	K562	blood:

Variant related genes	Relation type
ENSG00000111877	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10080855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10456919	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1087453	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1087454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1087455	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11153785	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190974	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12191490	0.83[ASN][1000 genomes]
rs12191819	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195153	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12196440	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12197931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203353	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12203542	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12206826	0.97[ASN][1000 genomes]
rs12210027	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12212179	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214434	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12216519	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1321836	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1342793	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1407205	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407206	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418712	0.86[AMR][1000 genomes]
rs1539434	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1775619	0.91[AMR][1000 genomes]
rs2295709	0.82[ASN][1000 genomes]
rs2357022	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2782574	0.86[AMR][1000 genomes]
rs2797355	0.91[AMR][1000 genomes]
rs284914	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284915	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284916	0.83[ASN][1000 genomes]
rs284918	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284920	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs376225	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3798594	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798595	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798599	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388987	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs409849	0.84[ASN][1000 genomes]
rs41292550	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41292554	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946384	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55810806	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56794995	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56895036	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6935641	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937499	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs706971	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs706978	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs706979	0.80[EUR][1000 genomes]
rs72966811	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72966851	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72966873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72966896	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72970448	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs768995	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs768996	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768348	0.86[AMR][1000 genomes]
rs794250	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs794252	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs794253	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs794254	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs794259	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs794606	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794607	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794608	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794611	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs797002	0.80[EUR][1000 genomes]
rs797017	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs811201	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs811584	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9320673	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9374757	0.80[ASN][1000 genomes]
rs9387609	0.80[ASN][1000 genomes]
rs9481862	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9481867	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481868	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481869	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481870	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481872	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481877	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9481878	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9489530	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9489531	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9489535	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489536	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489537	0.97[ASN][1000 genomes]
rs9489539	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489541	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9489543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489544	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489547	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119216600-119243800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:119217000-119242200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:119218600-119247000	Strong transcription	Fetal Thymus	thymus
4	chr6:119219200-119254000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:119219200-119254400	Strong transcription	Placenta	Placenta
6	chr6:119219600-119253000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:119219600-119253800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:119221200-119255800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:119221400-119246800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:119221600-119237400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:119221600-119247800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:119222000-119243200	Strong transcription	HepG2	liver
13	chr6:119222000-119254000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:119222000-119254400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:119222000-119255200	Weak transcription	Fetal Heart	heart
16	chr6:119222200-119245400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:119222200-119253400	Strong transcription	Fetal Intestine Large	intestine
18	chr6:119222400-119246600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr6:119222400-119249600	Strong transcription	Primary B cells from peripheral blood	blood
20	chr6:119222600-119251400	Strong transcription	Dnd41	blood
21	chr6:119222600-119253800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:119222600-119253800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:119224000-119254000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:119224200-119245600	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:119224200-119246000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:119224200-119252800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr6:119224400-119245600	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr6:119224600-119254000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:119224800-119254800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:119225000-119238800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:119225400-119238600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:119226000-119255200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:119227000-119254800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:119227200-119241800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr6:119227400-119252000	Weak transcription	Small Intestine	intestine
36	chr6:119227400-119253800	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr6:119227600-119242600	Weak transcription	Stomach Mucosa	stomach
38	chr6:119227600-119247400	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr6:119227800-119239200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:119227800-119254800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr6:119228000-119253000	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr6:119228200-119253400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr6:119228400-119239000	Strong transcription	HMEC	breast
44	chr6:119229600-119238800	Weak transcription	NHLF	lung
45	chr6:119229600-119239400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:119230200-119238000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:119230400-119237400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr6:119230800-119237400	Strong transcription	Primary T cells from cord blood	blood
49	chr6:119231000-119241200	Weak transcription	Hela-S3	cervix
50	chr6:119231000-119243000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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