Variant report

Variant	rs7623123
Chromosome Location	chr3:20125788-20125789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:20120814..20122685-chr3:20125426..20127152,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11128936	1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12630578	0.82[ASN][1000 genomes]
rs12636325	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12639358	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17006625	0.83[CHD][hapmap]
rs1879775	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293139	1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2365362	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365370	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2365371	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623075	0.81[EUR][1000 genomes]
rs2661376	0.80[CEU][hapmap]
rs2661377	1.00[CEU][hapmap]
rs2686315	0.80[CEU][hapmap]
rs2929403	0.90[CEU][hapmap]
rs2948087	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs35562268	0.81[AFR][1000 genomes]
rs3804574	0.91[CEU][hapmap]
rs3942473	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6779759	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6784715	0.87[EUR][1000 genomes]
rs939851	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription 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 miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS 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 miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	esv1829018	chr3:20116077-20596244	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
13	esv1827700	chr3:20119716-20489086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
14	esv1830036	chr3:20121828-20278275	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
15	esv1830599	chr3:20121828-20375643	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7623123	RAB5A	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20102800-20136800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:20106800-20130800	Weak transcription	Fetal Intestine Large	intestine
3	chr3:20108200-20127600	Weak transcription	Ovary	ovary
4	chr3:20115400-20127200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:20116400-20194800	Weak transcription	NHDF-Ad	bronchial
6	chr3:20117200-20130800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr3:20118800-20129200	Weak transcription	Fetal Lung	lung
8	chr3:20121400-20127000	Weak transcription	Fetal Intestine Small	intestine
9	chr3:20122800-20131000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:20123000-20126800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:20123000-20127200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:20123000-20127400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:20123000-20127600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr3:20123000-20127800	Weak transcription	Right Atrium	heart
15	chr3:20123000-20131000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:20123000-20131600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:20123000-20137000	Weak transcription	Spleen	Spleen
18	chr3:20123000-20138400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:20123000-20140800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:20123000-20153000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:20123200-20126000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:20123200-20127000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:20123200-20127000	Weak transcription	Fetal Stomach	stomach
24	chr3:20123200-20127200	Weak transcription	Primary B cells from cord blood	blood
25	chr3:20123200-20127200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:20123200-20127200	Weak transcription	Aorta	Aorta
27	chr3:20123200-20127400	Weak transcription	Primary T cells from cord blood	blood
28	chr3:20123200-20127400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr3:20123200-20127400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr3:20123200-20127400	Weak transcription	Brain Anterior Caudate	brain
31	chr3:20123200-20127400	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:20123200-20127400	Weak transcription	Fetal Thymus	thymus
33	chr3:20123200-20127400	Weak transcription	Thymus	Thymus
34	chr3:20123200-20127400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr3:20123200-20127600	Weak transcription	Lung	lung
36	chr3:20123200-20129400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:20123200-20129400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:20123200-20129400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:20123200-20130200	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:20123200-20131000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:20123200-20131000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:20123200-20131000	Weak transcription	Adipose Nuclei	Adipose
43	chr3:20123200-20131000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr3:20123200-20131000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:20123200-20131000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:20123200-20131200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:20123200-20131200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:20123200-20131600	Weak transcription	Brain Substantia Nigra	brain
49	chr3:20123200-20132400	Weak transcription	Liver	Liver
50	chr3:20123200-20132800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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