Variant report

Variant	rs3940231
Chromosome Location	chr14:24748363-24748364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:24748117..24749826-chr14:24765905..24766674,5	MCF-7	breast:
2	chr14:24747479..24749144-chr14:24897627..24900068,2	MCF-7	breast:
3	chr14:24748208..24749586-chr14:24765690..24766775,9	MCF-7	breast:
4	chr14:24747459..24749153-chr14:24766216..24767743,2	MCF-7	breast:
5	chr14:24746982..24750097-chr14:24751993..24755047,3	K562	blood:
6	chr14:24746366..24751677-chr14:24760244..24766198,8	MCF-7	breast:
7	chr14:24747500..24749837-chr14:24779084..24781929,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139899	Chromatin interaction
ENSG00000213906	Chromatin interaction
ENSG00000213903	Chromatin interaction
ENSG00000157379	Chromatin interaction
ENSG00000136305	Chromatin interaction
ENSG00000100441	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11158621	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs14193	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075530	0.83[JPT][hapmap]
rs2281473	0.83[JPT][hapmap]
rs2295313	0.85[EUR][1000 genomes]
rs3825585	0.83[JPT][hapmap]
rs4982886	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982887	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6573653	0.83[JPT][hapmap]
rs729421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941502	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941503	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941505	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3940231	ANG	cis	parietal	SCAN
rs3940231	DHRS1	cis	cerebellum	SCAN
rs3940231	DHRS1	cis	parietal	SCAN
rs3940231	RABGGTA	Cis_1M	lymphoblastoid	RTeQTL
rs3940231	TSSK4	cis	parietal	SCAN
rs3940231	PSMB11	cis	parietal	SCAN
rs3940231	MYH6	cis	cerebellum	SCAN
rs3940231	RABGGTA	cis	multi-tissue	Pritchard
rs3940231	ADCY4	cis	cerebellum	SCAN
rs3940231	FAM158A	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24741200-24753200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:24741200-24758800	Weak transcription	Aorta	Aorta
3	chr14:24741200-24768200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:24741400-24748400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr14:24741400-24748400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr14:24741400-24748400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr14:24741400-24748400	Weak transcription	Brain Angular Gyrus	brain
8	chr14:24741400-24748400	Weak transcription	Brain Anterior Caudate	brain
9	chr14:24741400-24748400	Weak transcription	Psoas Muscle	Psoas
10	chr14:24741400-24748400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr14:24741400-24748400	Weak transcription	HSMM	muscle
12	chr14:24741400-24748800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr14:24741400-24748800	Weak transcription	Lung	lung
14	chr14:24741400-24749800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr14:24741400-24749800	Weak transcription	HSMMtube	muscle
16	chr14:24741400-24751800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr14:24741400-24752200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr14:24741400-24752200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr14:24741400-24757800	Weak transcription	Fetal Stomach	stomach
20	chr14:24741400-24758600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr14:24741400-24758800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr14:24741600-24749600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr14:24741600-24758400	Weak transcription	Fetal Intestine Large	intestine
24	chr14:24741600-24758600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr14:24741600-24758600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr14:24741600-24759200	Weak transcription	Small Intestine	intestine
27	chr14:24741600-24767800	Weak transcription	Fetal Brain Male	brain
28	chr14:24741800-24758800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr14:24742000-24758600	Weak transcription	Thymus	Thymus
30	chr14:24743400-24754600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr14:24743400-24758600	Weak transcription	Gastric	stomach
32	chr14:24743600-24748400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr14:24743800-24748400	Weak transcription	Liver	Liver
34	chr14:24743800-24758600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr14:24743800-24759000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr14:24744600-24750800	Enhancers	Esophagus	oesophagus
37	chr14:24744800-24748400	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr14:24744800-24749200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr14:24745000-24748400	Weak transcription	Fetal Intestine Small	intestine
40	chr14:24745000-24748400	Weak transcription	Left Ventricle	heart
41	chr14:24745000-24748600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr14:24745200-24756400	Weak transcription	HepG2	liver
43	chr14:24745200-24758800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr14:24745800-24749200	Enhancers	Primary hematopoietic stem cells	blood
45	chr14:24746000-24749000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr14:24746000-24751800	Enhancers	Primary B cells from peripheral blood	blood
47	chr14:24746000-24752000	Enhancers	Primary B cells from cord blood	blood
48	chr14:24746200-24749400	Enhancers	Spleen	Spleen
49	chr14:24746200-24750800	Enhancers	Adipose Nuclei	Adipose
50	chr14:24746400-24751000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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