Variant report

Variant	rs1004704
Chromosome Location	chr16:48537421-48537422
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:48536818..48539436-chr16:48623109..48624985,2	K562	blood:
2	chr16:48418941..48420591-chr16:48536326..48538238,2	K562	blood:

Variant related genes	Relation type
ENSG00000196470	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2062553	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2062554	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4785244	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7184700	1.00[CHB][hapmap]
rs7198420	1.00[CHB][hapmap]
rs7206781	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs8046716	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs8052026	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs8063059	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap]
rs9921402	1.00[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061316	chr16:48264175-48594219	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers 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	38 gene(s)	inside rSNPs	diseases
2	esv1800739	chr16:48418505-48560315	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv428658	chr16:48438656-48587750	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv1817281	chr16:48509311-48537421	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv1842977	chr16:48509311-48537421	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv1849228	chr16:48509311-48537421	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1065358	chr16:48513824-48554254	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1064323	chr16:48531171-48573066	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv1060196	chr16:48531171-48578101	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1004704	NKD1	cis	cerebellum	SCAN
rs1004704	SNX20	cis	cerebellum	SCAN
rs1004704	PHKB	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48531000-48538600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr16:48531200-48538800	Enhancers	Fetal Stomach	stomach
3	chr16:48532400-48541800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr16:48533200-48537600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr16:48533200-48538200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr16:48533400-48539000	Enhancers	Fetal Lung	lung
7	chr16:48533800-48537600	Weak transcription	Placenta	Placenta
8	chr16:48534200-48537600	Weak transcription	NHDF-Ad	bronchial
9	chr16:48534400-48537600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr16:48534400-48537800	Weak transcription	NH-A	brain
11	chr16:48534400-48537800	Weak transcription	Osteobl	bone
12	chr16:48534400-48538000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr16:48534400-48539000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr16:48534600-48537600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr16:48535800-48537800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr16:48536000-48537600	Weak transcription	Colon Smooth Muscle	Colon
17	chr16:48536000-48537600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr16:48536200-48537600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr16:48536200-48538400	Weak transcription	Fetal Kidney	kidney
20	chr16:48536600-48537600	Weak transcription	Spleen	Spleen
21	chr16:48536800-48538200	Enhancers	Lung	lung
22	chr16:48537000-48537800	Enhancers	Right Atrium	heart
23	chr16:48537000-48538600	Enhancers	NHLF	lung
24	chr16:48537200-48538600	Enhancers	Adipose Nuclei	Adipose
25	chr16:48537200-48538600	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr16:48537200-48538800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr16:48537400-48537600	Enhancers	Duodenum Mucosa	Duodenum
28	chr16:48537400-48537600	Enhancers	Fetal Intestine Small	intestine
29	chr16:48537400-48537600	Enhancers	Left Ventricle	heart
30	chr16:48537400-48537600	Enhancers	Stomach Smooth Muscle	stomach
31	chr16:48537400-48537800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr16:48537400-48538400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr16:48537400-48538400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr16:48537400-48538400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr16:48537400-48538600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr16:48537400-48538600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr16:48537400-48538600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr16:48537400-48538800	Enhancers	Fetal Muscle Leg	muscle
39	chr16:48537400-48538800	Enhancers	Ovary	ovary

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