Variant report

Variant	rs1880024
Chromosome Location	chr4:8454639-8454640
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	chr4:8451706..8454826-chr4:8468396..8471846,3	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10461079	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1357481	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1543246	0.88[ASN][1000 genomes]
rs1880023	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1916326	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1949733	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2010758	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2140337	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2386227	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2450475	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2631731	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2631734	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2631735	1.00[CEU][hapmap];0.93[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs2631736	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631740	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631742	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2631743	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631744	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2631745	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631746	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2631754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631756	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2631758	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2631762	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631768	0.81[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs2688219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688223	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2688224	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2688227	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2688231	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2688233	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688242	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2688243	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688247	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3103067	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3103069	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3103070	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3103071	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3103072	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3103099	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4696828	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6447875	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6837429	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6845969	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6858542	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs868105	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs871768	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs940133	0.82[EUR][1000 genomes]
rs940134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs940136	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1880024	C4orf6	cis	cerebellum	SCAN
rs1880024	TBC1D14	cis	parietal	SCAN
rs1880024	TRMT44	cis	Nerve Tibial	GTEx
rs1880024	C4orf23	cis	cerebellum	SCAN
rs1880024	C4orf23	cis	parietal	SCAN
rs1880024	RP11-689P11.2	cis	lung	GTEx
rs1880024	STK32B	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8443600-8455400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:8444200-8456800	Weak transcription	A549	lung
3	chr4:8444400-8455400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:8444600-8455800	Weak transcription	NHDF-Ad	bronchial
5	chr4:8444800-8458400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:8445000-8454800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:8445000-8460800	Weak transcription	Psoas Muscle	Psoas
8	chr4:8445200-8461400	Weak transcription	Hela-S3	cervix
9	chr4:8445400-8455000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:8446400-8457400	Strong transcription	Fetal Intestine Small	intestine
11	chr4:8446400-8463200	Strong transcription	Stomach Smooth Muscle	stomach
12	chr4:8446400-8473800	Strong transcription	Fetal Stomach	stomach
13	chr4:8446600-8463600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:8446600-8463600	Strong transcription	Thymus	Thymus
15	chr4:8446600-8464600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:8446600-8473400	Strong transcription	Dnd41	blood
17	chr4:8446600-8474000	Strong transcription	Fetal Muscle Leg	muscle
18	chr4:8446800-8456800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr4:8446800-8463800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:8447000-8458200	Strong transcription	HepG2	liver
21	chr4:8447000-8461800	Strong transcription	Fetal Intestine Large	intestine
22	chr4:8447000-8464000	Strong transcription	Primary B cells from cord blood	blood
23	chr4:8447000-8474400	Strong transcription	Fetal Brain Female	brain
24	chr4:8447000-8475200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:8447000-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:8447200-8457400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:8447200-8458000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:8447200-8458200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr4:8447200-8464200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr4:8447200-8473000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr4:8447200-8480200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:8447400-8463600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:8447400-8474000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:8447400-8482200	Strong transcription	Primary T cells from cord blood	blood
35	chr4:8447600-8464000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:8447600-8472200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:8447600-8473400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr4:8447800-8458400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:8447800-8459800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:8447800-8461200	Strong transcription	Liver	Liver
41	chr4:8447800-8461800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:8447800-8463400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr4:8447800-8463400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:8447800-8463600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr4:8447800-8463800	Strong transcription	Brain Cingulate Gyrus	brain
46	chr4:8447800-8472800	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr4:8448000-8461400	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:8448000-8461600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr4:8448000-8461800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr4:8448000-8462000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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