Variant report

Variant	rs1450478
Chromosome Location	chr4:121837791-121837792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:121836736..121838271-chr4:121841875..121843483,2	MCF-7	breast:
2	chr4:121832110..121834901-chr4:121836477..121839157,3	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11931234	1.00[CHB][hapmap]
rs11935242	0.92[CHB][hapmap]
rs11939905	0.92[CHB][hapmap]
rs11942389	0.92[CHB][hapmap]
rs1450476	0.85[CHB][hapmap]
rs17051268	0.85[CHB][hapmap]
rs17051269	0.92[CHB][hapmap]
rs17051270	0.85[CHB][hapmap]
rs17051274	0.92[CHB][hapmap]
rs17051280	1.00[CHB][hapmap]
rs2667188	0.85[CHB][hapmap]
rs4833688	0.83[CHB][hapmap]
rs6534219	0.88[YRI][hapmap]
rs6844456	0.85[MKK][hapmap];0.92[YRI][hapmap]
rs885460	0.92[CHB][hapmap]

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	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1450478	SAMD9	trans	lymphoblastoid	RTeQTL
rs1450478	D4S234E	trans	lymphoblastoid	seeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121798200-121842400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:121812000-121839400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:121812800-121839800	Weak transcription	Psoas Muscle	Psoas
4	chr4:121813400-121839400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:121813400-121841600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr4:121813600-121839800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:121813800-121842400	Weak transcription	NHEK	skin
8	chr4:121814200-121839800	Weak transcription	Pancreas	Pancrea
9	chr4:121814600-121840000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:121814600-121842600	Weak transcription	Right Ventricle	heart
11	chr4:121815200-121839800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:121818000-121842400	Weak transcription	NH-A	brain
13	chr4:121821000-121839800	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:121821200-121840000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:121821400-121839800	Weak transcription	Fetal Stomach	stomach
16	chr4:121823400-121837800	Weak transcription	Fetal Kidney	kidney
17	chr4:121823800-121842400	Weak transcription	HSMM	muscle
18	chr4:121824800-121840400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:121825000-121839800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:121825000-121839800	Weak transcription	Osteobl	bone
21	chr4:121825000-121842600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:121825200-121838200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:121825200-121839200	Weak transcription	Fetal Intestine Small	intestine
24	chr4:121825200-121839800	Weak transcription	Aorta	Aorta
25	chr4:121825600-121842400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:121827600-121842400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:121827800-121837800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:121828000-121839800	Weak transcription	NHDF-Ad	bronchial
29	chr4:121829600-121839400	Weak transcription	Fetal Intestine Large	intestine
30	chr4:121830600-121838000	Weak transcription	Left Ventricle	heart
31	chr4:121830600-121838000	Weak transcription	Ovary	ovary
32	chr4:121830600-121839400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr4:121833600-121839800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:121834200-121839000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr4:121834800-121838000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:121834800-121838000	Weak transcription	Fetal Lung	lung
37	chr4:121835800-121838400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:121836000-121837800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:121836000-121838400	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr4:121836400-121838400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:121836600-121838400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:121836600-121838800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:121836800-121838000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr4:121836800-121840000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr4:121837000-121838000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr4:121837000-121838200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:121837000-121842800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr4:121837200-121837800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr4:121837200-121839800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr4:121837200-121839800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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