Variant report

Variant	rs13102298
Chromosome Location	chr4:57241362-57241363
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57240891..57243438-chr4:57250107..57253288,3	K562	blood:
2	chr17:79824304..79826888-chr4:57240277..57242789,2	MCF-7	breast:
3	chr4:57241127..57243438-chr4:57250107..57253054,2	K562	blood:

Variant related genes	Relation type
ENSG00000141522	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000262413	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11728110	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11930159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13102012	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13124696	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13134963	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13135046	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13147132	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13150159	0.89[EUR][1000 genomes]
rs2030364	0.88[EUR][1000 genomes]
rs2176785	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554347	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6854758	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7694439	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9996468	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13102298	AASDH	cis	Skin Sun Exposed Lower leg	GTEx
rs13102298	AASDH	cis	multi-tissue	Pritchard
rs13102298	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs13102298	AASDH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
2	chr4:57202800-57252400	Weak transcription	NHDF-Ad	bronchial
3	chr4:57203000-57252600	Weak transcription	Right Ventricle	heart
4	chr4:57203200-57251800	Weak transcription	A549	lung
5	chr4:57203400-57252400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:57204000-57252200	Weak transcription	NH-A	brain
7	chr4:57204200-57252200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:57204800-57251800	Weak transcription	Fetal Brain Male	brain
9	chr4:57207800-57253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:57211000-57251600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:57211800-57252200	Weak transcription	Fetal Heart	heart
12	chr4:57212400-57251800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr4:57213000-57244200	Weak transcription	Spleen	Spleen
14	chr4:57213400-57251600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr4:57213400-57252200	Weak transcription	NHLF	lung
16	chr4:57213600-57250200	Weak transcription	K562	blood
17	chr4:57213600-57252000	Weak transcription	HMEC	breast
18	chr4:57214400-57251800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:57214600-57252200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:57215800-57251600	Weak transcription	Brain Anterior Caudate	brain
21	chr4:57216000-57251800	Weak transcription	HepG2	liver
22	chr4:57216000-57252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:57216000-57253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:57216200-57245600	Weak transcription	Colon Smooth Muscle	Colon
25	chr4:57216200-57246000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:57216200-57246200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:57216400-57251800	Weak transcription	Psoas Muscle	Psoas
28	chr4:57220600-57243400	Weak transcription	HSMM	muscle
29	chr4:57223000-57253200	Weak transcription	Esophagus	oesophagus
30	chr4:57223200-57253200	Weak transcription	Gastric	stomach
31	chr4:57223600-57251600	Weak transcription	Fetal Kidney	kidney
32	chr4:57225000-57243600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:57225000-57252200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr4:57226600-57245800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:57227400-57252400	Weak transcription	NHEK	skin
36	chr4:57229800-57244000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:57229800-57248200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr4:57229800-57251800	Weak transcription	Thymus	Thymus
39	chr4:57229800-57252400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:57229800-57252400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:57229800-57252400	Weak transcription	Brain Germinal Matrix	brain
42	chr4:57229800-57253000	Weak transcription	Ovary	ovary
43	chr4:57229800-57253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:57229800-57253200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:57232800-57246800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr4:57232800-57252400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:57232800-57252400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:57232800-57253000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:57235200-57244400	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr4:57235600-57252400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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