Variant report

Variant	rs944946
Chromosome Location	chr9:86300269-86300270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86298986..86303456-chr9:86320609..86324425,4	MCF-7	breast:
2	chr9:86294745..86296646-chr9:86298711..86300362,2	K562	blood:
3	chr18:40222756..40225050-chr9:86298792..86300940,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254473	Chromatin interaction
ENSG00000135018	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10115799	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10119344	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10125432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1035274	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1044175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10746718	0.95[ASN][1000 genomes]
rs10746719	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746720	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746721	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10780621	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10868040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868045	0.95[ASN][1000 genomes]
rs11140209	0.82[ASN][1000 genomes]
rs1333863	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333865	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360685	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1961952	0.81[EUR][1000 genomes]
rs1968216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2042042	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2058912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2542775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2542776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780997	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2780998	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2780999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2781000	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2781001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2781003	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811919	0.89[ASN][1000 genomes]
rs2811922	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811923	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811924	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2811925	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811926	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811927	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811928	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4146741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242623	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4454364	0.82[ASN][1000 genomes]
rs4877263	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4877796	0.82[ASN][1000 genomes]
rs4877798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559739	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7023082	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7039019	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7469301	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7850944	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7860614	0.82[ASN][1000 genomes]
rs7863266	0.81[ASN][1000 genomes]
rs7865296	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874980	0.95[ASN][1000 genomes]
rs961807	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv893513	chr9:86298632-86433459	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86260600-86300400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr9:86273800-86304000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:86280400-86307400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:86289000-86304200	Weak transcription	Ovary	ovary
5	chr9:86289000-86308200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:86289000-86321800	Weak transcription	Esophagus	oesophagus
7	chr9:86291400-86314400	Weak transcription	Fetal Heart	heart
8	chr9:86291600-86300600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:86292800-86308600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr9:86293600-86301200	Weak transcription	Aorta	Aorta
11	chr9:86293600-86301400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr9:86293600-86304200	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:86293600-86317000	Weak transcription	NHLF	lung
14	chr9:86294000-86321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:86294200-86305800	Weak transcription	Spleen	Spleen
16	chr9:86294200-86314200	Weak transcription	Gastric	stomach
17	chr9:86294200-86315600	Weak transcription	Right Ventricle	heart
18	chr9:86294200-86320000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:86295000-86301400	Weak transcription	Fetal Kidney	kidney
20	chr9:86295000-86308800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr9:86295000-86313600	Weak transcription	Lung	lung
22	chr9:86296000-86304000	Weak transcription	NHDF-Ad	bronchial
23	chr9:86296000-86320800	Weak transcription	Fetal Brain Female	brain
24	chr9:86296200-86316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr9:86296400-86303000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr9:86296400-86304200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr9:86296600-86303800	Weak transcription	Brain Substantia Nigra	brain
28	chr9:86296800-86301400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr9:86296800-86302200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr9:86296800-86303200	Weak transcription	Brain Germinal Matrix	brain
31	chr9:86296800-86306400	Weak transcription	Colon Smooth Muscle	Colon
32	chr9:86296800-86314200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr9:86297000-86301200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:86297000-86301400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr9:86297000-86304000	Weak transcription	Brain Angular Gyrus	brain
36	chr9:86297000-86304000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr9:86297000-86315600	Weak transcription	HMEC	breast
38	chr9:86297000-86315600	Weak transcription	HSMM	muscle
39	chr9:86297000-86320000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr9:86297200-86305400	Weak transcription	Psoas Muscle	Psoas
41	chr9:86297400-86301600	Weak transcription	Primary T cells from cord blood	blood
42	chr9:86297600-86302600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr9:86297600-86305400	Weak transcription	Left Ventricle	heart
44	chr9:86297600-86305400	Weak transcription	Small Intestine	intestine
45	chr9:86297600-86310800	Weak transcription	Fetal Lung	lung
46	chr9:86297600-86314400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr9:86297600-86319800	Weak transcription	Fetal Muscle Leg	muscle
48	chr9:86297600-86321200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:86297800-86303800	Weak transcription	Adipose Nuclei	Adipose
50	chr9:86297800-86305000	Weak transcription	Osteobl	bone

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