Variant report

Variant	rs2385860
Chromosome Location	chr3:46910618-46910619
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46910106..46910730-chr3:46950930..46951702,2	MCF-7	breast:
2	chr3:46905861..46908182-chr3:46909321..46912349,4	K562	blood:
3	chr3:46908943..46910828-chr3:46926732..46928602,2	K562	blood:
4	chr3:46908049..46912169-chr3:46912978..46916098,5	K562	blood:
5	chr3:46910116..46910779-chr3:47412321..47413311,2	K562	blood:
6	chr3:46909467..46911881-chr3:46954858..46956855,2	K562	blood:
7	chr3:46904622..46907361-chr3:46908422..46910821,2	K562	blood:

Variant related genes	Relation type
ENSG00000160808	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1042973	1.00[CHB][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap]
rs12106917	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs12107311	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs12486015	0.86[CHB][hapmap]
rs12492369	0.86[CHB][hapmap]
rs12493158	0.86[CHB][hapmap]
rs1531136	0.92[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1869868	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2227294	0.92[ASW][hapmap];0.93[CEU][hapmap];0.86[GIH][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs3792558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683304	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs57459864	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6763438	0.86[CHB][hapmap]
rs6768252	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs6777190	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs67839338	0.83[AMR][1000 genomes]
rs6797059	0.85[CHB][hapmap]
rs6801048	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs7614762	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs7633581	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs877670	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs936175	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv590205	chr3:46852679-46929546	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1003979	chr3:46853374-46943854	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv590206	chr3:46873957-46935527	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv876753	chr3:46884552-46957298	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv590207	chr3:46903361-46919379	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2385860	CYP8B1	cis	cerebellum	SCAN
rs2385860	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs2385860	SCAP	cis	parietal	SCAN
rs2385860	TMIE	cis	parietal	SCAN
rs2385860	HYAL2	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46904600-46911600	Enhancers	Placenta	Placenta
2	chr3:46905200-46911400	Enhancers	Fetal Lung	lung
3	chr3:46906000-46911600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr3:46906800-46920000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:46907800-46910800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:46908400-46911000	Enhancers	Brain Hippocampus Middle	brain
7	chr3:46908400-46911200	Enhancers	Ovary	ovary
8	chr3:46908400-46913200	Enhancers	Liver	Liver
9	chr3:46908600-46911000	Weak transcription	Fetal Kidney	kidney
10	chr3:46908800-46914000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:46909000-46911200	Enhancers	Adipose Nuclei	Adipose
12	chr3:46909000-46912200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:46909200-46912200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr3:46909400-46911000	Enhancers	HepG2	liver
15	chr3:46909600-46913400	Weak transcription	Aorta	Aorta
16	chr3:46909600-46917000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr3:46909800-46911000	Bivalent Enhancer	Fetal Stomach	stomach
18	chr3:46909800-46911000	Weak transcription	Pancreas	Pancrea
19	chr3:46909800-46913400	Weak transcription	Brain Anterior Caudate	brain
20	chr3:46909800-46914600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr3:46910000-46911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:46910000-46911000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:46910000-46911000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:46910000-46911000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:46910000-46911000	Weak transcription	Spleen	Spleen
26	chr3:46910000-46912200	Weak transcription	Lung	lung
27	chr3:46910000-46916400	Weak transcription	Brain Substantia Nigra	brain
28	chr3:46910000-46916400	Weak transcription	Psoas Muscle	Psoas
29	chr3:46910000-46916800	Weak transcription	Brain Angular Gyrus	brain
30	chr3:46910200-46911000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:46910200-46911000	Weak transcription	Left Ventricle	heart
32	chr3:46910200-46911000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr3:46910200-46916800	Weak transcription	Esophagus	oesophagus
34	chr3:46910400-46911200	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr3:46910400-46912200	Weak transcription	Fetal Heart	heart
36	chr3:46910400-46912400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:46910400-46914200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:46910400-46915200	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:46910600-46911000	Weak transcription	Right Ventricle	heart
40	chr3:46910600-46911200	Enhancers	Stomach Smooth Muscle	stomach
41	chr3:46910600-46915600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:46910600-46916600	Enhancers	Right Atrium	heart
43	chr3:46910600-46918400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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