Variant report

Variant	rs4578863
Chromosome Location	chr2:113090047-113090048
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr2:113089932-113090218	HepG2	liver:	n/a	n/a
2	E2F4	chr2:113090034-113090181	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr2:113089962-113090153	IMR90	lung:	n/a	n/a
4	CEBPB	chr2:113090016-113090159	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113032266..113035570-chr2:113088065..113092560,6	MCF-7	breast:
2	chr2:113032909..113035758-chr2:113089627..113091636,2	K562	blood:

Variant related genes	Relation type
ENSG00000248341	TF binding region
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10167748	0.96[ASN][1000 genomes]
rs10175234	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10177573	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10183121	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs10191002	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10203614	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10203843	0.96[ASN][1000 genomes]
rs10205038	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs10205897	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10211300	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs10439391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10864903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11123132	0.94[CHB][hapmap];1.00[YRI][hapmap]
rs11123135	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11123136	0.93[ASN][1000 genomes]
rs11674953	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs11691431	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11896500	0.94[ASN][1000 genomes]
rs11903741	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11904424	0.91[ASN][1000 genomes]
rs12464478	0.85[ASN][1000 genomes]
rs12464895	1.00[YRI][hapmap]
rs12711738	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12711739	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13387611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs34471791	0.86[ASN][1000 genomes]
rs4258804	0.96[ASN][1000 genomes]
rs4299347	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[MEX][hapmap];0.86[MKK][hapmap];1.00[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]
rs4332934	0.96[ASN][1000 genomes]
rs4352239	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4392265	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4399734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4419238	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4430968	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4446076	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4450606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4450607	0.95[ASN][1000 genomes]
rs4456711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4507112	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4522611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4525706	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4539797	0.96[ASN][1000 genomes]
rs4542853	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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4622729	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4630773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849058	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58337061	0.96[ASN][1000 genomes]
rs62160223	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6542045	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs6542051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6542052	0.91[ASN][1000 genomes]
rs6542053	1.00[ASN][1000 genomes]
rs6542054	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706874	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs6708164	0.97[ASN][1000 genomes]
rs6716010	0.85[EUR][1000 genomes]
rs6725933	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6726412	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6733138	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6744364	0.98[ASN][1000 genomes]
rs6751146	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6758110	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6761599	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71414636	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7557281	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7557862	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7564052	0.96[ASN][1000 genomes]
rs7569894	1.00[ASN][1000 genomes]
rs7571435	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7579561	0.98[ASN][1000 genomes]
rs7591439	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7598168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7599041	0.96[ASN][1000 genomes]
rs7600338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7601200	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[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601888	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8179708	0.94[ASN][1000 genomes]

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	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic 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	37 gene(s)	inside rSNPs	diseases
5	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv874870	chr2:113021811-113097699	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4578863	RGPD8	cis	Muscle Skeletal	GTEx
rs4578863	TMEM87B	cis	parietal	SCAN
rs4578863	POLR1B	cis	cerebellum	SCAN
rs4578863	RGPD8	cis	Artery Tibial	GTEx
rs4578863	FBLN7	cis	parietal	SCAN
rs4578863	POLR1B	cis	parietal	SCAN
rs4578863	RGPD8	cis	lung	GTEx
rs4578863	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs4578863	RGPD8	cis	Nerve Tibial	GTEx
rs4578863	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113034400-113097000	Weak transcription	Psoas Muscle	Psoas
2	chr2:113050600-113090600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:113057000-113099400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:113058200-113090600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:113059200-113096800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:113060000-113090600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:113060400-113090600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:113062200-113094400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:113062400-113090600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:113068200-113101400	Weak transcription	NHDF-Ad	bronchial
11	chr2:113069000-113097000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:113070000-113093600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:113075400-113094400	Weak transcription	NHLF	lung
14	chr2:113079800-113093200	Weak transcription	HSMM	muscle
15	chr2:113081400-113091200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:113081800-113092200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:113082200-113091800	Weak transcription	GM12878-XiMat	blood
18	chr2:113082200-113094200	Weak transcription	Small Intestine	intestine
19	chr2:113082200-113097000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:113082200-113097000	Weak transcription	Gastric	stomach
21	chr2:113082800-113091000	Weak transcription	HSMMtube	muscle
22	chr2:113083000-113097000	Weak transcription	Pancreas	Pancrea
23	chr2:113083400-113096400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:113084800-113091600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:113085800-113092800	Weak transcription	Fetal Intestine Small	intestine
26	chr2:113085800-113103600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:113086000-113090800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:113086000-113091400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr2:113086000-113092600	Weak transcription	Liver	Liver
30	chr2:113086000-113093000	Weak transcription	Fetal Brain Male	brain
31	chr2:113086000-113097000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:113088200-113090200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr2:113089000-113091200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:113089200-113090800	Weak transcription	Brain Substantia Nigra	brain
35	chr2:113089200-113090800	Weak transcription	Dnd41	blood
36	chr2:113089200-113091800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:113089200-113093000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:113089200-113097600	Weak transcription	Fetal Kidney	kidney
39	chr2:113089400-113090200	Strong transcription	Brain Germinal Matrix	brain
40	chr2:113089400-113091000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:113089400-113091000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:113089400-113091200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:113089400-113103400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:113089600-113091200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:113089600-113091200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:113089600-113091200	Weak transcription	Osteobl	bone
47	chr2:113089600-113091400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr2:113089600-113091600	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:113089600-113092000	Weak transcription	Right Ventricle	heart
50	chr2:113089600-113094400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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