Variant report

Variant	rs1517598
Chromosome Location	chr4:16020664-16020665
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16892805	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2531156	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2677782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2677783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2677788	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2677791	0.93[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55666771	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv916742	chr4:15797994-16064232	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1517598	C1QTNF7	cis	parietal	SCAN
rs1517598	REG1B	trans	lymphoblastoid	RTeQTL
rs1517598	LCORL	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15964600-16031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:15988400-16033800	Weak transcription	Pancreas	Pancrea
3	chr4:15989000-16024200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:15991000-16029000	Weak transcription	Stomach Mucosa	stomach
5	chr4:15992800-16024800	Weak transcription	Fetal Intestine Small	intestine
6	chr4:16003400-16024600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:16003400-16027000	Weak transcription	Right Ventricle	heart
8	chr4:16004000-16021000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:16004200-16027600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:16004400-16021000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:16004600-16027800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:16005400-16027200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:16006600-16027200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:16007000-16022200	Strong transcription	Primary hematopoietic stem cells	blood
15	chr4:16007000-16027000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr4:16007000-16030800	Weak transcription	Fetal Kidney	kidney
17	chr4:16008000-16033000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:16008400-16021400	Weak transcription	Aorta	Aorta
19	chr4:16008400-16025000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr4:16009200-16033200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:16010800-16038600	Weak transcription	Placenta	Placenta
22	chr4:16011000-16023400	Weak transcription	Fetal Brain Female	brain
23	chr4:16012000-16021000	Weak transcription	Right Atrium	heart
24	chr4:16012200-16026600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:16013200-16024800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:16013200-16025000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:16013400-16030800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:16014400-16027200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:16014600-16027000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr4:16015000-16021600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr4:16015400-16031200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:16016000-16024600	Weak transcription	Colonic Mucosa	Colon
33	chr4:16018200-16030800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:16019600-16021000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:16019600-16027400	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr4:16019800-16020800	Strong transcription	Fetal Muscle Leg	muscle
37	chr4:16019800-16021000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:16019800-16021200	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr4:16019800-16021200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr4:16019800-16026200	Strong transcription	Fetal Muscle Trunk	muscle
41	chr4:16020400-16020800	Bivalent Enhancer	GM12878-XiMat	blood
42	chr4:16020400-16022000	Enhancers	HSMMtube	muscle
43	chr4:16020400-16023200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr4:16020400-16023600	Enhancers	Fetal Brain Male	brain
45	chr4:16020600-16023200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr4:16020600-16023200	Weak transcription	Fetal Stomach	stomach
47	chr4:16020600-16023400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:16020600-16024800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr4:16020600-16024800	Weak transcription	Left Ventricle	heart
50	chr4:16020600-16025000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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