Variant report

Variant	rs2670624
Chromosome Location	chr4:89977728-89977729
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	chr4:89743956..89746323-chr4:89976893..89978969,2	K562	blood:
2	chr4:89977166..89979264-chr4:90032025..90033904,2	K562	blood:

Variant related genes	Relation type
ENSG00000138640	Chromatin interaction
ENSG00000271359	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1060693	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11097215	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs12647382	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13143981	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1343921	0.83[CHD][hapmap];0.96[GIH][hapmap];0.81[TSI][hapmap]
rs1398947	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1458558	0.85[CHD][hapmap];0.89[JPT][hapmap]
rs1513807	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1513824	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1533291	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1708660	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1708661	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1708674	0.89[JPT][hapmap]
rs1708675	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1708678	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1708679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1708680	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1708682	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1708684	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1795721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795728	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1795731	0.83[CHD][hapmap];0.89[JPT][hapmap]
rs1795732	0.89[JPT][hapmap]
rs1795733	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1807870	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1818494	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2037036	0.89[JPT][hapmap];0.82[TSI][hapmap]
rs2037037	0.89[JPT][hapmap]
rs2458545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2464513	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2670625	0.89[JPT][hapmap]
rs2670626	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2670629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28498689	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2869987	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs59610544	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60535906	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62308652	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6532094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6844490	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs6846926	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7440590	0.83[CEU][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs7691983	0.83[CEU][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs9307062	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs938266	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938268	0.83[CEU][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2670624	SPARCL1	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89944200-89978000	Weak transcription	Pancreas	Pancrea
2	chr4:89973400-89977800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:89973400-89977800	Weak transcription	Right Ventricle	heart
4	chr4:89973600-89977800	Weak transcription	Placenta	Placenta
5	chr4:89975200-89979200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:89975600-89977800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:89975600-89978400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:89975600-89978800	Active TSS	Duodenum Mucosa	Duodenum
9	chr4:89975800-89978400	Active TSS	H1 Cell Line	embryonic stem cell
10	chr4:89975800-89978800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:89976000-89978400	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr4:89976000-89978800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr4:89976000-89978800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:89976000-89978800	Active TSS	Aorta	Aorta
15	chr4:89976000-89978800	Active TSS	Right Atrium	heart
16	chr4:89976200-89978600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:89976200-89978600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:89976200-89978800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:89976200-89978800	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr4:89976200-89978800	Active TSS	Ovary	ovary
21	chr4:89976400-89978400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:89976400-89978800	Active TSS	HMEC	breast
23	chr4:89976600-89978400	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr4:89976600-89978400	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr4:89976600-89978600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr4:89976600-89978600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:89976600-89978600	Active TSS	A549	lung
28	chr4:89976600-89978600	Active TSS	NHLF	lung
29	chr4:89976600-89978800	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr4:89976600-89978800	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr4:89976600-89978800	Flanking Active TSS	HUVEC	blood vessel
32	chr4:89976600-89979000	Active TSS	Stomach Smooth Muscle	stomach
33	chr4:89976600-89979000	Active TSS	K562	blood
34	chr4:89976800-89978200	Active TSS	GM12878-XiMat	blood
35	chr4:89976800-89978600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:89976800-89978600	Active TSS	HSMMtube	muscle
37	chr4:89976800-89978800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:89976800-89978800	Active TSS	Fetal Kidney	kidney
39	chr4:89976800-89978800	Active TSS	Fetal Muscle Leg	muscle
40	chr4:89977000-89978600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:89977000-89978600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:89977000-89978600	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr4:89977000-89978600	Active TSS	Hela-S3	cervix
44	chr4:89977000-89978800	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr4:89977000-89978800	Active TSS	Adipose Nuclei	Adipose
46	chr4:89977000-89978800	Active TSS	Brain Hippocampus Middle	brain
47	chr4:89977000-89978800	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr4:89977000-89978800	Active TSS	Fetal Brain Male	brain
49	chr4:89977000-89978800	Active TSS	Fetal Intestine Small	intestine
50	chr4:89977000-89978800	Active TSS	Fetal Muscle Trunk	muscle

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