Variant report

Variant	rs1529625
Chromosome Location	chr2:38945701-38945702
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38805084..38807176-chr2:38944983..38947545,2	K562	blood:
2	chr2:38944533..38947216-chr2:38977421..38979282,2	K562	blood:
3	chr2:38938428..38940592-chr2:38945131..38949430,3	K562	blood:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10173118	0.81[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs10197412	0.85[CEU][hapmap];0.82[CHB][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap]
rs10865143	0.88[CEU][hapmap];0.91[CHB][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs11124645	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1138974	0.82[AMR][1000 genomes]
rs1138975	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11898812	0.91[CHB][hapmap]
rs12618118	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs12621103	0.82[CHB][hapmap]
rs12712614	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13011311	0.80[AMR][1000 genomes]
rs13024811	0.82[CHB][hapmap]
rs1530852	0.84[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs1530853	0.88[CEU][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs17494049	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1965751	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1968411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1979143	0.82[CHB][hapmap]
rs1997377	0.92[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2037875	0.85[CEU][hapmap];0.82[CHB][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap]
rs2272445	0.87[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes]
rs3097713	0.82[CHB][hapmap]
rs3099968	0.82[CHB][hapmap]
rs3112159	0.89[JPT][hapmap]
rs3112183	0.91[CHB][hapmap]
rs3112184	0.91[CHB][hapmap]
rs3112188	0.91[CHB][hapmap]
rs3112189	0.91[CHB][hapmap]
rs3112191	0.91[CHB][hapmap]
rs3112192	0.91[CHB][hapmap]
rs3112196	0.91[CHB][hapmap]
rs3112200	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs3134637	0.91[CHB][hapmap]
rs35182980	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35682042	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731838	0.82[CHB][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4602206	0.88[CEU][hapmap]
rs4630748	0.88[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs4670891	0.82[AMR][1000 genomes]
rs6715866	0.88[CEU][hapmap];0.82[CHB][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs6717670	0.91[CHB][hapmap]
rs6728394	0.91[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs6731386	0.80[AMR][1000 genomes]
rs6746818	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6756847	0.87[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs67716743	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7419616	0.88[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs7419838	0.81[CEU][hapmap]
rs7581263	0.80[AMR][1000 genomes]
rs7581653	0.80[AMR][1000 genomes]
rs7596239	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7603676	0.87[MEX][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv1800555	chr2:38929745-38950126	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1830359	chr2:38929745-38950126	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv1797820	chr2:38941956-38972456	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv3459539	chr2:38944736-38947192	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3459540	chr2:38944736-38947192	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv820974	chr2:38945458-38972971	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv828975	chr2:38945666-38946367	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1529625	DHX57	cis	cerebellum	SCAN
rs1529625	MORN2	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38894400-38960600	Weak transcription	Brain Substantia Nigra	brain
2	chr2:38894800-38949400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:38905000-38947600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:38909200-38947800	Weak transcription	Right Ventricle	heart
5	chr2:38909400-38960600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:38909600-38947800	Weak transcription	Brain Anterior Caudate	brain
7	chr2:38910000-38948000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:38914600-38948000	Weak transcription	Spleen	Spleen
9	chr2:38915800-38947200	Weak transcription	Ovary	ovary
10	chr2:38918000-38949400	Weak transcription	Primary B cells from cord blood	blood
11	chr2:38918600-38947600	Weak transcription	Hela-S3	cervix
12	chr2:38918600-38956800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:38920400-38947800	Weak transcription	Esophagus	oesophagus
14	chr2:38921400-38947400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:38927400-38947600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:38927600-38957000	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:38928200-38947800	Weak transcription	Stomach Mucosa	stomach
18	chr2:38928800-38971600	Weak transcription	Small Intestine	intestine
19	chr2:38930000-38946800	Weak transcription	Right Atrium	heart
20	chr2:38930000-38956600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:38930600-38947000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:38930600-38965000	Weak transcription	Gastric	stomach
23	chr2:38931200-38948600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:38932400-38947600	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:38932600-38947800	Weak transcription	Pancreas	Pancrea
26	chr2:38932800-38947000	Weak transcription	Lung	lung
27	chr2:38932800-38956800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:38933200-38947600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:38933800-38947800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr2:38934800-38947600	Weak transcription	K562	blood
31	chr2:38936400-38957200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:38936400-38960600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr2:38936400-38968400	Weak transcription	Colonic Mucosa	Colon
34	chr2:38936800-38946000	Weak transcription	Thymus	Thymus
35	chr2:38937200-38956600	Weak transcription	Fetal Brain Female	brain
36	chr2:38937600-38947600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:38937600-38970400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:38937800-38947600	Weak transcription	GM12878-XiMat	blood
39	chr2:38938000-38949400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:38938000-38949400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:38938200-38947200	Weak transcription	Fetal Stomach	stomach
42	chr2:38938400-38948600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:38939000-38945800	Weak transcription	Fetal Thymus	thymus
44	chr2:38939000-38947000	Weak transcription	Fetal Lung	lung
45	chr2:38939000-38947800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:38939000-38947800	Weak transcription	Fetal Brain Male	brain
47	chr2:38939000-38956600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:38939200-38946000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:38939200-38947200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:38939200-38948000	Weak transcription	Fetal Kidney	kidney

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