Variant report

Variant	rs9840990
Chromosome Location	chr3:105191096-105191097
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105186048..105188294-chr3:105188492..105191411,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1044243	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs13315085	0.86[AMR][1000 genomes]
rs13315918	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs13317140	0.86[AMR][1000 genomes]
rs13317379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13320956	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs13325976	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17181561	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17181701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189101	0.86[AMR][1000 genomes]
rs17189643	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs17189711	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2291374	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs28452673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772552	0.86[AMR][1000 genomes]
rs72989914	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs72989943	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs73006164	0.91[AMR][1000 genomes]
rs751554	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610031	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7619149	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7633779	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7645474	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9288807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822014	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825097	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9826369	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828587	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9829190	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9830049	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9831077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839346	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9841699	0.86[AMR][1000 genomes]
rs9842815	0.82[AMR][1000 genomes]
rs9843750	0.82[AMR][1000 genomes]
rs9847971	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9851399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854028	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855810	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9859198	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859785	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9862725	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9866561	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870312	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9873424	0.86[AMR][1000 genomes]
rs9876895	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9876906	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877002	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877483	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878315	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9882494	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990253	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv877304	chr3:105122214-105198374	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105179000-105191400	Weak transcription	HSMM	muscle
2	chr3:105179000-105192200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:105179600-105192400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:105185200-105193000	Weak transcription	Aorta	Aorta
5	chr3:105185800-105192400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:105186200-105192200	Weak transcription	Brain Angular Gyrus	brain
7	chr3:105186200-105194000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:105186400-105191400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:105186400-105191400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:105186400-105192200	Weak transcription	A549	lung
11	chr3:105189600-105191600	Enhancers	HUVEC	blood vessel
12	chr3:105189800-105192200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:105189800-105192600	Enhancers	Brain Substantia Nigra	brain
14	chr3:105189800-105192800	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr3:105190000-105191200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:105190000-105191200	Weak transcription	NH-A	brain
17	chr3:105190000-105191200	Weak transcription	Osteobl	bone
18	chr3:105190000-105192200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:105190200-105191400	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:105190200-105192200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:105190200-105192400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:105190400-105192200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:105190400-105192200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:105190400-105192400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:105190400-105192400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:105190600-105194000	Enhancers	Brain Anterior Caudate	brain
27	chr3:105190800-105191400	Enhancers	H1 Cell Line	embryonic stem cell
28	chr3:105190800-105191400	Enhancers	Brain Cingulate Gyrus	brain
29	chr3:105190800-105192200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:105191000-105191400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:105191000-105191600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:105191000-105192200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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