Variant report

Variant	rs3821023
Chromosome Location	chr2:38893660-38893661
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38892007..38895113-chr2:38976994..38979857,4	K562	blood:
2	chr2:38824811..38832919-chr2:38891494..38898299,16	K562	blood:
3	chr2:38825670..38832919-chr2:38891527..38903424,21	K562	blood:
4	chr2:38818005..38820191-chr2:38893287..38895221,2	K562	blood:
5	chr2:38829496..38831232-chr2:38893143..38894875,2	MCF-7	breast:
6	chr2:38891861..38895889-chr2:38976029..38979857,7	K562	blood:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000235586	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11688977	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689051	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478924	0.94[EUR][1000 genomes]
rs12712609	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011383	0.93[EUR][1000 genomes]
rs13029674	0.93[EUR][1000 genomes]
rs13387464	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425086	0.95[EUR][1000 genomes]
rs2373424	0.94[EUR][1000 genomes]
rs28551538	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs34533539	0.85[EUR][1000 genomes]
rs4670263	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670882	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670883	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6707543	0.85[EUR][1000 genomes]
rs6732137	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6736380	0.85[EUR][1000 genomes]
rs6744400	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6761563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7571326	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7574493	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588762	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590750	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590835	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590926	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597535	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv581485	chr2:38839323-38893660	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv873882	chr2:38858669-38921498	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv873883	chr2:38881106-38932777	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3821023	GALM	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38892600-38893800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:38892600-38894000	Active TSS	Fetal Intestine Large	intestine
3	chr2:38892600-38894400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:38892800-38893800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:38892800-38893800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr2:38892800-38893800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr2:38892800-38893800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:38892800-38893800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr2:38892800-38893800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:38892800-38893800	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr2:38892800-38893800	Active TSS	Primary T killer memory cells from peripheral blood	blood
12	chr2:38892800-38893800	Active TSS	Brain Angular Gyrus	brain
13	chr2:38892800-38893800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:38892800-38893800	Flanking Active TSS	Placenta	Placenta
15	chr2:38892800-38893800	Active TSS	Placenta Amnion	Placenta Amnion
16	chr2:38892800-38893800	Active TSS	Psoas Muscle	Psoas
17	chr2:38892800-38893800	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr2:38892800-38893800	Flanking Active TSS	NHEK	skin
19	chr2:38892800-38893800	Active TSS	NHLF	lung
20	chr2:38892800-38894000	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr2:38892800-38894000	Active TSS	Colon Smooth Muscle	Colon
22	chr2:38892800-38894000	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr2:38892800-38894000	Active TSS	Fetal Kidney	kidney
24	chr2:38892800-38894000	Active TSS	Fetal Stomach	stomach
25	chr2:38892800-38894000	Active TSS	Lung	lung
26	chr2:38892800-38894000	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr2:38892800-38894000	Bivalent/Poised TSS	HepG2	liver
28	chr2:38892800-38894200	Active TSS	H1 Cell Line	embryonic stem cell
29	chr2:38892800-38894200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:38892800-38894200	Flanking Active TSS	Primary B cells from peripheral blood	blood
31	chr2:38892800-38894200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr2:38892800-38894200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:38892800-38894400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:38892800-38894400	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr2:38892800-38894400	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr2:38892800-38894400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr2:38892800-38894400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr2:38892800-38894400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:38892800-38894400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:38892800-38894400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:38892800-38894400	Active TSS	Aorta	Aorta
42	chr2:38892800-38894400	Active TSS	Brain Anterior Caudate	brain
43	chr2:38892800-38894400	Active TSS	Brain Cingulate Gyrus	brain
44	chr2:38892800-38894400	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr2:38892800-38894400	Flanking Active TSS	Fetal Thymus	thymus
46	chr2:38892800-38894400	Active TSS	Ovary	ovary
47	chr2:38892800-38894400	Active TSS	Pancreas	Pancrea
48	chr2:38892800-38894400	Active TSS	Right Ventricle	heart
49	chr2:38892800-38894600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr2:38892800-38894600	Flanking Active TSS	GM12878-XiMat	blood

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