Variant report

Variant	rs3798599
Chromosome Location	chr6:119223999-119224000
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119220803..119224279-chr6:119253648..119257104,3	K562	blood:
2	chr6:119220702..119224795-chr6:119249246..119252141,5	K562	blood:
3	chr6:119222754..119224280-chr6:119255028..119257218,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253194	Chromatin interaction
ENSG00000111877	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10080855	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10456919	0.80[EUR][1000 genomes]
rs1087453	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1087454	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1087455	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11153785	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190974	0.80[EUR][1000 genomes]
rs12191490	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12191819	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194515	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195153	0.80[EUR][1000 genomes]
rs12196440	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12197931	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200499	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203353	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12203542	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12206826	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12210027	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12212179	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214434	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12216519	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1321836	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1342793	0.80[EUR][1000 genomes]
rs1407205	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539434	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2295709	0.82[ASN][1000 genomes]
rs2357022	0.80[EUR][1000 genomes]
rs284914	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284915	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284916	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs284918	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284920	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs376225	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3798594	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388987	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs409849	0.84[ASN][1000 genomes]
rs41292550	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41292554	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946384	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55810806	0.80[EUR][1000 genomes]
rs56794995	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56895036	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6935641	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937499	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs706971	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs706978	0.80[EUR][1000 genomes]
rs706979	0.80[EUR][1000 genomes]
rs72966811	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72966851	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72966873	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72966896	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72970448	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs768995	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs768996	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs794250	0.80[EUR][1000 genomes]
rs794252	0.80[EUR][1000 genomes]
rs794253	0.80[EUR][1000 genomes]
rs794254	0.80[EUR][1000 genomes]
rs794259	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	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs797002	0.80[EUR][1000 genomes]
rs797017	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs811201	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs811584	0.80[EUR][1000 genomes]
rs9320673	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9374757	0.80[ASN][1000 genomes]
rs9387609	0.80[ASN][1000 genomes]
rs9481862	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9481867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481868	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481869	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481870	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481871	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481872	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481877	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9481878	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9489530	0.86[EUR][1000 genomes]
rs9489531	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9489535	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489536	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489537	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9489539	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489540	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489541	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9489543	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489544	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489547	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119216600-119224400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:119216600-119233800	Weak transcription	Lung	lung
3	chr6:119216600-119236600	Weak transcription	Gastric	stomach
4	chr6:119216600-119243800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:119216800-119230600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:119216800-119232400	Weak transcription	Colonic Mucosa	Colon
7	chr6:119216800-119232600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:119216800-119233200	Weak transcription	Aorta	Aorta
9	chr6:119216800-119235800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:119217000-119225400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:119217000-119242200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:119217800-119224200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr6:119217800-119224400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:119217800-119224600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:119217800-119228400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:119217800-119236200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr6:119218200-119229200	Weak transcription	NHLF	lung
18	chr6:119218600-119247000	Strong transcription	Fetal Thymus	thymus
19	chr6:119218800-119237200	Strong transcription	Primary hematopoietic stem cells	blood
20	chr6:119219200-119225400	Weak transcription	Small Intestine	intestine
21	chr6:119219200-119254000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr6:119219200-119254400	Strong transcription	Placenta	Placenta
23	chr6:119219600-119253000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:119219600-119253800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr6:119219800-119224200	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr6:119220000-119224200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:119220400-119226400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr6:119220600-119224400	Weak transcription	Left Ventricle	heart
29	chr6:119220600-119225400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr6:119220600-119226200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr6:119220600-119227000	Weak transcription	Spleen	Spleen
32	chr6:119220600-119233200	Weak transcription	Pancreas	Pancrea
33	chr6:119220600-119234400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:119220600-119236600	Weak transcription	Esophagus	oesophagus
35	chr6:119220800-119224200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:119220800-119224400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:119220800-119225400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr6:119220800-119233000	Weak transcription	Fetal Intestine Small	intestine
39	chr6:119220800-119233600	Weak transcription	Right Ventricle	heart
40	chr6:119221000-119228000	Weak transcription	Hela-S3	cervix
41	chr6:119221200-119224200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr6:119221200-119224800	Genic enhancers	NH-A	brain
43	chr6:119221200-119255800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:119221400-119224600	Weak transcription	Fetal Brain Male	brain
45	chr6:119221400-119246800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:119221600-119236600	Weak transcription	Psoas Muscle	Psoas
47	chr6:119221600-119237400	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:119221600-119247800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:119221800-119224400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:119221800-119224800	Strong transcription	Primary T cells fromperipheralblood	blood

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