Variant report

Variant	rs8328
Chromosome Location	chr1:224346959-224346960
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:224312506..224315473-chr1:224345868..224347563,2	K562	blood:
2	chr1:224345362..224348351-chr1:224369651..224372388,2	K562	blood:
3	chr1:224344874..224349477-chr1:224369651..224372388,4	K562	blood:
4	chr1:224335933..224338116-chr1:224346191..224348944,2	K562	blood:
5	chr1:224227960..224229471-chr1:224345929..224348019,2	K562	blood:
6	chr1:224301857..224303494-chr1:224346848..224349418,2	K562	blood:
7	chr1:224339407..224345322-chr1:224346058..224350848,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143753	Chromatin interaction
ENSG00000143756	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10753454	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799478	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10799480	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10799505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916301	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916307	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916320	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916355	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916367	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10916403	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916415	0.87[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11808787	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12038372	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12049583	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12070670	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12076788	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12563153	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12730611	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13374070	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492694	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16844819	0.89[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.91[ASN][1000 genomes]
rs17560970	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1826421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2011117	0.81[CHB][hapmap]
rs2014782	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2048997	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2051105	0.90[ASN][1000 genomes]
rs2172361	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2280291	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2404843	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2896985	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3767730	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3820482	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820483	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653563	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653568	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs4653972	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653991	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653994	0.87[ASN][1000 genomes]
rs4653995	0.85[ASN][1000 genomes]
rs4654003	0.81[CHB][hapmap]
rs55664906	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55736782	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61827699	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426139	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6426143	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426169	0.93[ASN][1000 genomes]
rs6426178	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs66506223	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6657467	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6658494	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6659234	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6680651	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6681673	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6682292	0.81[CHB][hapmap]
rs6682551	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685405	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6685783	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6688818	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6690695	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6691405	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6698041	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6700284	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7511895	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7518839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7524705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7526252	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7542293	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7546235	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs869945	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs908795	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs908801	0.81[CHB][hapmap]
rs997296	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs997297	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv1792939	chr1:224336636-224351023	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	n/a
6	nsv945321	chr1:224344064-224347532	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8328	ENSG00000143756	cis	multi-tissue	Pritchard
rs8328	BPNT1	cis	parietal	SCAN
rs8328	FBXO28	cis	multi-tissue	Pritchard
rs8328	FBXO28	Cis_1M	lymphoblastoid	RTeQTL
rs8328	FBXO28	cis	lymphoblastoid	seeQTL
rs8328	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224303000-224363400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:224316600-224352200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:224325000-224351000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:224327600-224356400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:224335800-224349600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr1:224338400-224349200	Strong transcription	Primary B cells from peripheral blood	blood
7	chr1:224339000-224350000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:224339200-224363200	Weak transcription	Brain Angular Gyrus	brain
9	chr1:224340200-224348400	Strong transcription	Fetal Thymus	thymus
10	chr1:224340800-224347600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:224340800-224348200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:224340800-224349000	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:224341000-224349800	Strong transcription	Fetal Intestine Large	intestine
14	chr1:224341600-224349200	Strong transcription	A549	lung
15	chr1:224342600-224348400	Strong transcription	Primary T cells from cord blood	blood
16	chr1:224342800-224348600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:224343000-224348200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:224343000-224350000	Strong transcription	Liver	Liver
19	chr1:224343000-224350200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:224343000-224350200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:224343000-224350200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:224343200-224347000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:224343200-224348200	Strong transcription	Hela-S3	cervix
24	chr1:224343200-224348400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:224343200-224348400	Strong transcription	Colon Smooth Muscle	Colon
26	chr1:224343200-224348400	Strong transcription	Fetal Kidney	kidney
27	chr1:224343200-224350000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:224343200-224350000	Strong transcription	Primary B cells from cord blood	blood
29	chr1:224343200-224350000	Strong transcription	HSMM	muscle
30	chr1:224343200-224350200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:224343200-224350200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:224343200-224350200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:224343200-224350600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:224343400-224347200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:224343400-224347400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:224343400-224347600	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:224343400-224348200	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr1:224343400-224348400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:224343400-224348400	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr1:224343400-224348400	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:224343400-224348800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:224343400-224348800	Strong transcription	Dnd41	blood
43	chr1:224343400-224349200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr1:224343400-224350000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:224343400-224350200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:224343400-224350200	Strong transcription	Adipose Nuclei	Adipose
47	chr1:224343400-224350200	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:224343400-224350200	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr1:224343600-224347600	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr1:224343600-224348200	Strong transcription	Rectal Mucosa Donor 31	rectum

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