Variant report

Variant	rs4238331
Chromosome Location	chr15:59012133-59012134
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59007785..59010098-chr15:59010167..59012488,3	K562	blood:
2	chr15:59007785..59010313-chr15:59010988..59013487,2	K562	blood:
3	chr15:58993902..58996648-chr15:59011876..59013960,2	K562	blood:

Variant related genes	Relation type
ENSG00000199730	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11855190	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28391588	0.89[CHD][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs4774311	0.82[JPT][hapmap]
rs7163515	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7164844	0.82[JPT][hapmap]
rs7164954	0.81[ASN][1000 genomes]
rs7170538	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs7171198	0.82[JPT][hapmap]
rs7183504	0.86[ASN][1000 genomes]
rs8023706	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs8023946	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8027998	0.89[CHD][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs8039696	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9788674	0.81[JPT][hapmap]

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	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	esv1843037	chr15:59005922-59115159	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4238331	SLTM	cis	parietal	SCAN
rs4238331	CCNB2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58977200-59039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:58983200-59016600	Weak transcription	Small Intestine	intestine
3	chr15:58986600-59016600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr15:58989800-59016800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:58990000-59023400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:58991800-59012200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:58992000-59015800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr15:58992000-59023000	Weak transcription	Esophagus	oesophagus
9	chr15:58992000-59023800	Weak transcription	Aorta	Aorta
10	chr15:58992600-59016600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:58992600-59021000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr15:58994400-59012400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:58994400-59016400	Weak transcription	Adipose Nuclei	Adipose
14	chr15:58996000-59016600	Weak transcription	Colonic Mucosa	Colon
15	chr15:58996200-59016800	Weak transcription	Psoas Muscle	Psoas
16	chr15:58996600-59016600	Weak transcription	NHLF	lung
17	chr15:58996600-59016800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:58998400-59016600	Weak transcription	Osteobl	bone
19	chr15:58998600-59016600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:58998600-59016800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr15:58999000-59013600	Weak transcription	Right Ventricle	heart
22	chr15:58999000-59023800	Weak transcription	Gastric	stomach
23	chr15:59000600-59012200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:59002400-59016200	Weak transcription	Left Ventricle	heart
25	chr15:59003400-59016400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr15:59003800-59012400	Strong transcription	Fetal Thymus	thymus
27	chr15:59003800-59016600	Weak transcription	NH-A	brain
28	chr15:59004000-59013000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:59004200-59015600	Weak transcription	Colon Smooth Muscle	Colon
30	chr15:59005200-59022400	Weak transcription	Fetal Muscle Leg	muscle
31	chr15:59005600-59021600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr15:59005600-59023000	Weak transcription	Spleen	Spleen
33	chr15:59005600-59023600	Weak transcription	NHEK	skin
34	chr15:59005800-59022800	Weak transcription	HMEC	breast
35	chr15:59005800-59025200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr15:59006200-59023800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:59006200-59024000	Weak transcription	Pancreas	Pancrea
38	chr15:59006400-59013000	Weak transcription	Brain Hippocampus Middle	brain
39	chr15:59006400-59014400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr15:59006400-59016200	Weak transcription	Lung	lung
41	chr15:59006400-59016600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr15:59006400-59016800	Weak transcription	HSMMtube	muscle
43	chr15:59006400-59017000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:59006400-59017000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr15:59006400-59021600	Weak transcription	Fetal Stomach	stomach
46	chr15:59006400-59022800	Weak transcription	Fetal Intestine Small	intestine
47	chr15:59006600-59014800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:59007400-59026400	Weak transcription	Fetal Intestine Large	intestine
49	chr15:59008000-59014600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr15:59008200-59016200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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