Variant report

Variant	rs3813402
Chromosome Location	chr14:55257590-55257591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:55031208..55035304-chr14:55253192..55258095,4	K562	blood:
2	chr14:55049587..55051973-chr14:55255815..55258211,2	K562	blood:
3	chr14:55255469..55258062-chr14:55260338..55262456,2	K562	blood:

Variant related genes	Relation type
ENSG00000020577	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10136563	0.99[ASN][1000 genomes]
rs10137337	0.81[EUR][1000 genomes]
rs10138916	0.99[ASN][1000 genomes]
rs1040877	1.00[ASN][1000 genomes]
rs1114050	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1114051	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11158024	0.86[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11431	0.89[ASW][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs12586289	0.89[ASN][1000 genomes]
rs12886870	0.98[ASN][1000 genomes]
rs12887011	0.98[ASN][1000 genomes]
rs2181049	1.00[ASN][1000 genomes]
rs2281650	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2281652	0.84[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2295824	0.91[JPT][hapmap]
rs4402472	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4409990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4506812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4508355	0.99[ASN][1000 genomes]
rs4516125	0.99[ASN][1000 genomes]
rs4898855	0.80[ASN][1000 genomes]
rs4901541	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs4901542	0.82[JPT][hapmap]
rs4901547	0.98[ASN][1000 genomes]
rs6572975	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs6572976	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6572977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6572978	0.98[ASN][1000 genomes]
rs6572980	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs709939	0.80[ASW][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7143189	0.82[JPT][hapmap]
rs7148657	0.99[ASN][1000 genomes]
rs7150628	0.81[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7151853	0.99[ASN][1000 genomes]
rs7153975	0.99[ASN][1000 genomes]
rs7155922	0.82[JPT][hapmap]
rs7158665	0.82[JPT][hapmap]
rs8006657	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8011598	0.99[ASN][1000 genomes]
rs8011837	0.98[ASN][1000 genomes]
rs8011848	0.98[ASN][1000 genomes]
rs8013211	0.98[ASN][1000 genomes]
rs8021151	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.99[ASN][1000 genomes]
rs8021325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8021957	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.99[ASN][1000 genomes]
rs8022503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs911614	0.84[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs911615	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs927379	0.99[ASN][1000 genomes]
rs927380	0.99[ASN][1000 genomes]
rs927381	0.99[ASN][1000 genomes]
rs927382	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.99[ASN][1000 genomes]
rs927383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530042	chr14:55208170-55386966	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3813402	SAMD4A	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55237600-55261200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr14:55240800-55259200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr14:55240800-55261600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr14:55240800-55261600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr14:55241000-55258400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:55241000-55259200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr14:55241000-55260200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr14:55241000-55263200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr14:55241200-55257600	Weak transcription	K562	blood
10	chr14:55241200-55272200	Weak transcription	A549	lung
11	chr14:55243600-55261400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr14:55243800-55258000	Strong transcription	HUVEC	blood vessel
13	chr14:55244000-55258200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr14:55244200-55257800	Strong transcription	HSMMtube	muscle
15	chr14:55244200-55258000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr14:55244200-55258200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr14:55244400-55259400	Strong transcription	NHLF	lung
18	chr14:55244800-55257800	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr14:55246600-55259400	Strong transcription	NHDF-Ad	bronchial
20	chr14:55247000-55257600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr14:55247200-55258000	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr14:55250000-55258000	Strong transcription	Rectal Smooth Muscle	rectum
23	chr14:55250000-55258800	Weak transcription	Primary B cells from cord blood	blood
24	chr14:55250400-55257800	Strong transcription	Fetal Stomach	stomach
25	chr14:55250600-55258600	Weak transcription	Colonic Mucosa	Colon
26	chr14:55250600-55259000	Strong transcription	Adipose Nuclei	Adipose
27	chr14:55250600-55259000	Weak transcription	Fetal Lung	lung
28	chr14:55250800-55258000	Strong transcription	HepG2	liver
29	chr14:55251000-55258000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr14:55251400-55258200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr14:55251600-55258000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr14:55251800-55258000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr14:55252000-55257800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr14:55252000-55258200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr14:55252400-55258000	Strong transcription	Colon Smooth Muscle	Colon
36	chr14:55252400-55259600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr14:55252800-55258200	Strong transcription	HSMM	muscle
38	chr14:55253400-55258000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr14:55253600-55257600	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr14:55253800-55259200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr14:55253800-55259400	Strong transcription	Aorta	Aorta
42	chr14:55254000-55258800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr14:55254000-55258800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr14:55254000-55259000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr14:55254200-55258800	Weak transcription	Brain Substantia Nigra	brain
46	chr14:55254200-55260600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr14:55254400-55260200	Weak transcription	Psoas Muscle	Psoas
48	chr14:55254600-55257800	Strong transcription	Osteobl	bone
49	chr14:55254600-55261400	Weak transcription	NH-A	brain
50	chr14:55254800-55258000	Strong transcription	HMEC	breast

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