Variant report

Variant	rs9489535
Chromosome Location	chr6:119219098-119219099
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:119218770-119219424	K562	blood:	n/a	n/a
2	POLR2A	chr6:119218907-119219598	H1-hESC	embryonic stem cell:	n/a	n/a
3	SPI1	chr6:119218955-119219276	GM12891	blood:	n/a	chr6:119219160-119219169
4	SPI1	chr6:119219043-119219273	GM12878	blood:	n/a	chr6:119219160-119219169
5	SPI1	chr6:119218929-119219279	GM12891	blood:	n/a	chr6:119219160-119219169
6	SPI1	chr6:119219056-119219266	GM12878	blood:	n/a	chr6:119219160-119219169

No.	Distal block	Cell Line	Cell type
1	chr6:119214552..119219906-chr6:119253918..119257622,8	MCF-7	breast:
2	chr6:119213105..119220728-chr6:119253299..119257962,22	K562	blood:
3	chr6:119213694..119219544-chr6:119251621..119258172,21	K562	blood:
4	chr6:119215906..119219234-chr6:119443291..119446175,3	K562	blood:
5	chr6:119217885..119221356-chr6:119243903..119247955,3	K562	blood:
6	chr6:119218879..119223837-chr6:119239300..119242721,4	K562	blood:
7	chr6:119217885..119219986-chr6:119244920..119246613,2	K562	blood:
8	chr6:119216161..119219506-chr6:119398191..119401599,4	K562	blood:

Variant related genes	Relation type
MCM9	TF binding region
ENSG00000111879	Chromatin interaction
ENSG00000111877	Chromatin interaction
ENSG00000253194	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10080855	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10456919	0.80[EUR][1000 genomes]
rs1087453	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1087454	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1087455	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11153785	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189950	1.00[CEU][hapmap];0.93[CHB][hapmap]
rs12190974	0.80[EUR][1000 genomes]
rs12191490	0.83[ASN][1000 genomes]
rs12191819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194515	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195153	0.80[EUR][1000 genomes]
rs12195334	0.93[CHB][hapmap]
rs12196440	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12197931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200499	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203353	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12203542	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12204929	1.00[CEU][hapmap];0.93[CHB][hapmap]
rs12206826	1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs12210027	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12212179	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214434	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12216519	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1321836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1342793	0.80[EUR][1000 genomes]
rs1407205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407206	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539434	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1775619	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap]
rs2051056	0.82[JPT][hapmap]
rs2051057	0.86[JPT][hapmap]
rs2295709	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2357022	0.80[EUR][1000 genomes]
rs284914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[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	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284920	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs376225	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3798594	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798599	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388987	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs409849	0.84[ASN][1000 genomes]
rs41292550	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41292554	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946383	0.82[JPT][hapmap]
rs4946384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];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	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6910327	0.81[CHB][hapmap]
rs6935641	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937499	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs706971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs706978	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs706979	0.80[EUR][1000 genomes]
rs72966811	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72966851	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72966873	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72966896	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72970448	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs768995	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs768996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745460	0.93[CHB][hapmap]
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	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs794606	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794608	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794611	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794614	0.82[JPT][hapmap]
rs797002	0.80[EUR][1000 genomes]
rs797017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs811201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9481867	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481868	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481869	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];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	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9489526	0.91[YRI][hapmap]
rs9489530	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9489531	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9489536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489537	1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs9489539	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489540	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489541	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9489543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489547	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs962393	0.80[CHB][hapmap];0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1023826	chr6:119026481-119221408	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119216600-119219600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:119216600-119220200	Weak transcription	Pancreas	Pancrea
3	chr6:119216600-119220200	Weak transcription	Spleen	Spleen
4	chr6:119216600-119220400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:119216600-119220400	Weak transcription	Esophagus	oesophagus
6	chr6:119216600-119224400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:119216600-119233800	Weak transcription	Lung	lung
8	chr6:119216600-119236600	Weak transcription	Gastric	stomach
9	chr6:119216600-119243800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:119216800-119219200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr6:119216800-119219200	Weak transcription	Placenta	Placenta
12	chr6:119216800-119219600	Weak transcription	HSMM	muscle
13	chr6:119216800-119220200	Weak transcription	Right Ventricle	heart
14	chr6:119216800-119230600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:119216800-119232400	Weak transcription	Colonic Mucosa	Colon
16	chr6:119216800-119232600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:119216800-119233200	Weak transcription	Aorta	Aorta
18	chr6:119216800-119235800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr6:119217000-119220200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:119217000-119223200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr6:119217000-119225400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:119217000-119242200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:119217200-119219400	Enhancers	Colon Smooth Muscle	Colon
24	chr6:119217600-119219200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr6:119217600-119220200	Weak transcription	Brain Hippocampus Middle	brain
26	chr6:119217600-119221600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:119217600-119221800	Enhancers	Ovary	ovary
28	chr6:119217600-119222600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr6:119217800-119219200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:119217800-119219200	Enhancers	Fetal Lung	lung
31	chr6:119217800-119219200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr6:119217800-119219400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:119217800-119219600	Weak transcription	Fetal Stomach	stomach
34	chr6:119217800-119219800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr6:119217800-119219800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr6:119217800-119219800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:119217800-119219800	Weak transcription	Fetal Intestine Large	intestine
38	chr6:119217800-119220000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:119217800-119220000	Weak transcription	Brain Angular Gyrus	brain
40	chr6:119217800-119220000	Weak transcription	Osteobl	bone
41	chr6:119217800-119220200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:119217800-119220200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr6:119217800-119220200	Weak transcription	Hela-S3	cervix
44	chr6:119217800-119220400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr6:119217800-119220400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr6:119217800-119221000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:119217800-119221000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr6:119217800-119221400	Weak transcription	Adipose Nuclei	Adipose
49	chr6:119217800-119221600	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr6:119217800-119221800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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