Variant report

Variant	rs3802439
Chromosome Location	chr9:98776111-98776112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98770544..98772627-chr9:98774325..98776534,2	K562	blood:
2	chr9:98774733..98776824-chr9:98788412..98790252,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225194	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10512243	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512244	0.85[GIH][hapmap];0.93[TSI][hapmap]
rs1410297	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16910291	0.83[CEU][hapmap];0.90[AMR][1000 genomes]
rs16910302	0.83[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes]
rs16910370	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs16910376	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16910382	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16910396	0.85[GIH][hapmap];0.87[TSI][hapmap]
rs17303045	0.88[AMR][1000 genomes]
rs17304942	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17305138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305917	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17394582	0.83[CEU][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs17394881	0.98[AMR][1000 genomes]
rs17396240	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396553	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396860	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972802	0.86[AMR][1000 genomes]
rs2026643	0.85[YRI][hapmap]
rs2149099	1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2149100	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2176026	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs4144585	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs55645821	0.84[EUR][1000 genomes]
rs55699149	0.90[AMR][1000 genomes]
rs55746108	0.90[AMR][1000 genomes]
rs55787215	0.87[EUR][1000 genomes]
rs55810950	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55923424	0.90[AMR][1000 genomes]
rs55983886	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56016781	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs56108623	0.98[AMR][1000 genomes]
rs56162045	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56217203	1.00[AMR][1000 genomes]
rs56225283	0.84[EUR][1000 genomes]
rs56379566	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56678652	1.00[AMR][1000 genomes]
rs62559011	0.90[AMR][1000 genomes]
rs62559012	0.90[AMR][1000 genomes]
rs62559013	0.90[AMR][1000 genomes]
rs62559025	0.90[AMR][1000 genomes]
rs62559027	0.90[AMR][1000 genomes]
rs62559029	0.93[AMR][1000 genomes]
rs62559030	0.93[AMR][1000 genomes]
rs62559031	0.93[AMR][1000 genomes]
rs62559053	0.98[AMR][1000 genomes]
rs62559054	1.00[AMR][1000 genomes]
rs62559055	1.00[AMR][1000 genomes]
rs62559057	1.00[AMR][1000 genomes]
rs62559058	0.98[AMR][1000 genomes]
rs62559059	1.00[AMR][1000 genomes]
rs62559760	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62559762	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559763	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559766	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559769	0.87[EUR][1000 genomes]
rs62559794	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62559796	0.84[EUR][1000 genomes]
rs62562960	1.00[AMR][1000 genomes]
rs62562961	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62562963	1.00[AMR][1000 genomes]
rs62562966	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562967	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562970	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562979	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562980	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562981	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562982	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562985	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562986	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562989	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62562992	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73532684	0.82[AMR][1000 genomes]
rs7864473	0.82[JPT][hapmap]

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	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98706400-98777400	Weak transcription	Psoas Muscle	Psoas
2	chr9:98714000-98782600	Weak transcription	HUVEC	blood vessel
3	chr9:98734600-98782400	Weak transcription	NHEK	skin
4	chr9:98735400-98778400	Weak transcription	Hela-S3	cervix
5	chr9:98736600-98778800	Weak transcription	Fetal Brain Male	brain
6	chr9:98741800-98778600	Weak transcription	NH-A	brain
7	chr9:98747800-98782800	Weak transcription	Fetal Kidney	kidney
8	chr9:98748000-98782600	Weak transcription	HMEC	breast
9	chr9:98748400-98782800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr9:98748600-98781200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr9:98759000-98780200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr9:98765000-98777600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:98765800-98781600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:98766400-98779800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:98766400-98780800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr9:98766600-98777400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:98766800-98776800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:98766800-98777000	Strong transcription	Fetal Muscle Leg	muscle
19	chr9:98766800-98777200	Strong transcription	Fetal Intestine Large	intestine
20	chr9:98767600-98777400	Strong transcription	Primary B cells from cord blood	blood
21	chr9:98768600-98782600	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:98769600-98776400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr9:98770200-98776200	Weak transcription	Colonic Mucosa	Colon
24	chr9:98770400-98776400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr9:98771200-98776600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr9:98771200-98777200	Strong transcription	HepG2	liver
27	chr9:98771200-98781200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr9:98771600-98776400	Weak transcription	Gastric	stomach
29	chr9:98771600-98776400	Weak transcription	Lung	lung
30	chr9:98771600-98778400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr9:98771600-98779200	Weak transcription	Fetal Brain Female	brain
32	chr9:98771600-98779600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:98771600-98779800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:98771600-98781600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr9:98771600-98782600	Weak transcription	Placenta	Placenta
36	chr9:98771600-98782800	Weak transcription	A549	lung
37	chr9:98771600-98783000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:98771800-98776400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:98771800-98776400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr9:98771800-98776400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:98771800-98777200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr9:98771800-98778800	Weak transcription	Osteobl	bone
43	chr9:98771800-98780800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr9:98771800-98781800	Weak transcription	Right Ventricle	heart
45	chr9:98771800-98782600	Weak transcription	Ovary	ovary
46	chr9:98772000-98779200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr9:98772000-98781400	Weak transcription	NHLF	lung
48	chr9:98772000-98781600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:98772200-98776400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr9:98772200-98777200	Strong transcription	HSMM	muscle

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