Variant report

Variant	rs3743478
Chromosome Location	chr15:77400388-77400389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:77399499..77401311-chr15:77835017..77836203,9	MCF-7	breast:
2	chr15:77397830..77402873-chr15:77403837..77409871,6	K562	blood:
3	chr15:77396281..77398389-chr15:77398942..77400984,2	K562	blood:
4	chr15:77399766..77400631-chr15:77835398..77836258,2	K562	blood:
5	chr15:77395363..77399207-chr15:77399512..77402124,4	MCF-7	breast:
6	chr15:77361896..77364276-chr15:77398497..77401504,3	MCF-7	breast:
7	chr15:77399950..77400942-chr15:77923445..77924282,3	MCF-7	breast:
8	chr15:77316407..77317258-chr15:77399611..77400626,4	MCF-7	breast:
9	chr15:77399717..77400658-chr15:77788766..77789797,3	MCF-7	breast:
10	chr15:77363355..77365975-chr15:77397364..77401294,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000140391	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11072643	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1125617	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11630689	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11632941	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11636648	0.81[JPT][hapmap]
rs11853287	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11853460	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11854193	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11857294	0.84[EUR][1000 genomes]
rs11858641	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs12443386	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900433	0.87[ASN][1000 genomes]
rs12901297	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12904088	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907847	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12908262	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12909924	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12913233	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12914128	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12916731	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1446312	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1823100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1867779	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2175941	0.83[EUR][1000 genomes]
rs28584877	0.80[EUR][1000 genomes]
rs3743479	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4243045	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4414462	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886511	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886849	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886856	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62008452	0.83[EUR][1000 genomes]
rs7163503	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7169831	0.81[JPT][hapmap]
rs7177533	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8026500	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8028571	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking 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	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv904414	chr15:77304310-77400388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
6	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3743478	HEXA	cis	cerebellum	SCAN
rs3743478	HMG20A	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77387000-77404200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:77390200-77404200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:77390400-77406400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:77393800-77403400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:77394600-77404200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:77394600-77413400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:77395200-77404800	Weak transcription	HepG2	liver
8	chr15:77396200-77401000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:77396200-77404200	Weak transcription	Fetal Lung	lung
10	chr15:77396400-77401200	Enhancers	Fetal Muscle Leg	muscle
11	chr15:77396600-77404800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:77397000-77404200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:77397600-77404200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:77397600-77405600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:77397600-77406200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:77397600-77411200	Weak transcription	HUVEC	blood vessel
17	chr15:77397800-77411400	Weak transcription	Fetal Thymus	thymus
18	chr15:77398000-77411600	Weak transcription	Fetal Brain Female	brain
19	chr15:77398200-77403000	Weak transcription	Spleen	Spleen
20	chr15:77398200-77405400	Weak transcription	Aorta	Aorta
21	chr15:77398400-77405600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:77399000-77400600	Enhancers	Adipose Nuclei	Adipose
23	chr15:77399000-77400800	Enhancers	Fetal Stomach	stomach
24	chr15:77399000-77400800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr15:77399000-77401200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:77399200-77400400	Enhancers	Colon Smooth Muscle	Colon
27	chr15:77399200-77400400	Enhancers	Stomach Smooth Muscle	stomach
28	chr15:77399200-77400600	Enhancers	Primary B cells from peripheral blood	blood
29	chr15:77399200-77400600	Enhancers	Brain Angular Gyrus	brain
30	chr15:77399200-77400600	Enhancers	Brain Substantia Nigra	brain
31	chr15:77399200-77400600	Enhancers	Fetal Muscle Trunk	muscle
32	chr15:77399200-77400600	Enhancers	Placenta	Placenta
33	chr15:77399200-77400600	Enhancers	Rectal Smooth Muscle	rectum
34	chr15:77399200-77400600	Enhancers	HSMM	muscle
35	chr15:77399200-77400800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:77399200-77400800	Enhancers	Brain Hippocampus Middle	brain
37	chr15:77399200-77400800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr15:77399200-77401000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:77399200-77401000	Enhancers	Brain Cingulate Gyrus	brain
40	chr15:77399200-77401000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:77399200-77401000	Enhancers	Fetal Kidney	kidney
42	chr15:77399200-77401000	Enhancers	NHDF-Ad	bronchial
43	chr15:77399200-77401000	Enhancers	Osteobl	bone
44	chr15:77399200-77401800	Enhancers	HSMMtube	muscle
45	chr15:77399400-77400400	Enhancers	Right Atrium	heart
46	chr15:77399400-77400600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:77399400-77400600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:77399400-77400600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr15:77399400-77400600	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr15:77399400-77400600	Enhancers	Left Ventricle	heart

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