Variant report

Variant	rs1648312
Chromosome Location	chr15:45457349-45457350
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:45444506..45446626-chr15:45455721..45457375,2	K562	blood:
2	chr15:45444538..45447388-chr15:45455721..45457816,3	K562	blood:
3	chr15:45456638..45458886-chr15:45696035..45698478,2	K562	blood:
4	chr15:45457275..45460718-chr15:45477484..45481344,4	K562	blood:
5	chr15:45457064..45458836-chr15:45462821..45464924,2	MCF-7	breast:
6	chr15:45449920..45453086-chr15:45456416..45459415,4	K562	blood:
7	chr15:45453899..45457914-chr15:45495194..45498173,3	K562	blood:
8	chr15:45456567..45458793-chr15:45475778..45478216,2	MCF-7	breast:
9	chr15:45454753..45457923-chr15:45490933..45493735,3	K562	blood:
10	chr15:45456315..45459130-chr15:45878271..45881206,2	K562	blood:
11	chr15:45457159..45458711-chr15:45469879..45471937,2	MCF-7	breast:
12	chr15:45457346..45461990-chr15:45488766..45494297,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259932	Chromatin interaction
ENSG00000138606	Chromatin interaction
ENSG00000171763	Chromatin interaction
ENSG00000260170	Chromatin interaction
ENSG00000260035	Chromatin interaction
ENSG00000104164	Chromatin interaction
ENSG00000137857	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1145089	1.00[JPT][hapmap]
rs1620253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648310	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648317	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706807	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706808	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706811	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706812	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706815	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1706817	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706827	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1706829	1.00[JPT][hapmap]
rs2162246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292468	1.00[CEU][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs2458237	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467819	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467820	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493143	1.00[JPT][hapmap]
rs7169193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv457124	chr15:45381998-45460422	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv569312	chr15:45381998-45460422	Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv1823029	chr15:45387102-45482245	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
8	nsv569313	chr15:45413541-45457458	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv518213	chr15:45421758-45464768	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv520580	chr15:45438537-45457349	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
11	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1648312	GATM	cis	lymphoblastoid	seeQTL
rs1648312	SHF	cis	cerebellum	SCAN
rs1648312	ADAL	cis	parietal	SCAN
rs1648312	SHF	cis	parietal	SCAN
rs1648312	CCNDBP1	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45427600-45458600	Weak transcription	Right Atrium	heart
2	chr15:45434800-45457800	Weak transcription	Adipose Nuclei	Adipose
3	chr15:45439000-45457800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:45439000-45458000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:45440400-45458600	Weak transcription	Aorta	Aorta
6	chr15:45441000-45458000	Weak transcription	Primary T cells from cord blood	blood
7	chr15:45441200-45458000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr15:45442200-45457600	Weak transcription	Small Intestine	intestine
9	chr15:45442400-45458000	Weak transcription	Primary B cells from cord blood	blood
10	chr15:45443400-45458000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:45444800-45457400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:45448400-45457800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:45449400-45458600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:45450400-45457400	Weak transcription	Fetal Brain Female	brain
15	chr15:45450800-45457400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:45451400-45458400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:45454800-45458600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:45455200-45457600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:45455400-45457600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr15:45455400-45457600	Weak transcription	Thymus	Thymus
21	chr15:45455400-45457800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:45455400-45457800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:45455400-45457800	Weak transcription	Colonic Mucosa	Colon
24	chr15:45455400-45457800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr15:45455400-45457800	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr15:45455400-45458000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr15:45455400-45458200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr15:45455400-45458200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr15:45455400-45458400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:45455400-45458600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:45455400-45458600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr15:45455400-45458600	Weak transcription	A549	lung
33	chr15:45455600-45457600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr15:45455600-45457600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:45455600-45457600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr15:45455600-45457800	Weak transcription	Brain Germinal Matrix	brain
37	chr15:45455600-45457800	Weak transcription	Fetal Intestine Large	intestine
38	chr15:45455600-45458200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:45455600-45458600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:45455600-45458600	Weak transcription	Placenta	Placenta
41	chr15:45455800-45457400	Weak transcription	Brain Anterior Caudate	brain
42	chr15:45455800-45457400	Strong transcription	Esophagus	oesophagus
43	chr15:45455800-45457400	Weak transcription	Left Ventricle	heart
44	chr15:45455800-45457600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr15:45455800-45457600	Weak transcription	Colon Smooth Muscle	Colon
46	chr15:45455800-45457800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr15:45455800-45457800	Weak transcription	Brain Substantia Nigra	brain
48	chr15:45455800-45457800	Weak transcription	Stomach Mucosa	stomach
49	chr15:45455800-45457800	Weak transcription	Spleen	Spleen
50	chr15:45455800-45458000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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