Variant report

Variant	rs10028291
Chromosome Location	chr4:76653383-76653384
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	POLR2A	chr4:76651510-76653519	K562	blood:	n/a	n/a
2	POLR2A	chr4:76653199-76653494	MCF10A-Er-Src	breast:	n/a	n/a
3	E2F4	chr4:76653224-76653434	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76580718..76583042-chr4:76652874..76655046,2	K562	blood:
2	chr4:76646646..76648324-chr4:76652983..76654497,2	K562	blood:

Variant related genes	Relation type
G3BP2	TF binding region
ENSG00000138757	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10016782	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10031352	0.85[AFR][1000 genomes]
rs10031616	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10033315	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10212995	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097075	0.81[EUR][1000 genomes]
rs11097112	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097113	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097122	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11727895	0.83[AFR][1000 genomes]
rs11728073	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11730896	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11932454	0.83[EUR][1000 genomes]
rs11938067	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11943497	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12505149	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12508992	0.83[AFR][1000 genomes]
rs13102733	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13110602	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13133144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13133472	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13134891	0.84[AMR][1000 genomes]
rs13145290	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13147276	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16996019	0.80[YRI][hapmap]
rs17000786	0.93[ASW][hapmap];0.91[LWK][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs2047989	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2055997	0.93[JPT][hapmap]
rs2271472	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2869175	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2904018	0.83[ASN][1000 genomes]
rs324690	0.93[ASW][hapmap];0.91[LWK][hapmap];0.84[YRI][hapmap]
rs324693	0.84[YRI][hapmap]
rs324703	0.83[YRI][hapmap]
rs324709	0.83[YRI][hapmap]
rs324713	0.81[AFR][1000 genomes]
rs324714	0.87[YRI][hapmap]
rs324722	0.80[AFR][1000 genomes]
rs324723	0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs324726	0.93[ASW][hapmap];0.91[LWK][hapmap];0.83[YRI][hapmap]
rs324727	0.93[ASW][hapmap];0.91[LWK][hapmap];0.84[YRI][hapmap]
rs324735	0.93[ASW][hapmap];0.91[LWK][hapmap];0.84[YRI][hapmap]
rs324740	0.93[ASW][hapmap];0.91[LWK][hapmap];0.84[YRI][hapmap]
rs3796479	0.85[CHD][hapmap]
rs3796481	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4262008	0.93[ASW][hapmap];0.89[LWK][hapmap];0.84[YRI][hapmap]
rs4446339	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859404	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4859405	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859406	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4859408	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4859409	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859549	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859552	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859554	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4859555	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55664143	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62318556	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6531901	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6829993	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6843016	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6845147	0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6846575	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6847333	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7655464	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7657198	0.80[AFR][1000 genomes]
rs7661037	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7665517	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7693127	0.83[AFR][1000 genomes]
rs905954	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs987561	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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	51 gene(s)	inside rSNPs	diseases
2	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10028291	FAM47E	cis	parietal	SCAN
rs10028291	SCARB2	cis	parietal	SCAN
rs10028291	CXCL10	cis	parietal	SCAN
rs10028291	PAQR3	cis	cerebellum	SCAN
rs10028291	CCNG2	cis	cerebellum	SCAN
rs10028291	PPEF2	cis	parietal	SCAN
rs10028291	CDKL2	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76650800-76658600	Weak transcription	Brain Substantia Nigra	brain
2	chr4:76650800-76673400	Weak transcription	Lung	lung
3	chr4:76650800-76675600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:76650800-76675800	Weak transcription	Esophagus	oesophagus
5	chr4:76650800-76737800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:76651000-76653600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr4:76651000-76653800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr4:76651000-76655200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:76651200-76657200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:76651200-76660800	Weak transcription	Thymus	Thymus
11	chr4:76651200-76661400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:76651200-76663600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:76651400-76653400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:76651400-76667000	Weak transcription	Gastric	stomach
15	chr4:76651800-76667000	Weak transcription	Primary B cells from cord blood	blood
16	chr4:76652000-76653400	Weak transcription	Left Ventricle	heart
17	chr4:76652000-76653400	Weak transcription	Pancreas	Pancrea
18	chr4:76652000-76653600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:76652000-76653600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr4:76652000-76653600	Active TSS	GM12878-XiMat	blood
21	chr4:76652000-76653800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:76652000-76654400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr4:76652000-76657200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:76652000-76660600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:76652000-76673400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr4:76652000-76675200	Weak transcription	Fetal Thymus	thymus
27	chr4:76652000-76675400	Weak transcription	Placenta	Placenta
28	chr4:76652000-76675600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr4:76652000-76675600	Weak transcription	Brain Hippocampus Middle	brain
30	chr4:76652000-76675600	Weak transcription	Spleen	Spleen
31	chr4:76652000-76696400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:76652200-76653400	Enhancers	HepG2	liver
33	chr4:76652200-76654400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:76652200-76654400	Weak transcription	Psoas Muscle	Psoas
35	chr4:76652200-76654800	Weak transcription	HSMMtube	muscle
36	chr4:76652200-76657200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:76652200-76659200	Weak transcription	Fetal Stomach	stomach
38	chr4:76652200-76660400	Weak transcription	Right Ventricle	heart
39	chr4:76652200-76664400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr4:76652200-76670800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr4:76652200-76675600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr4:76652400-76653400	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr4:76652400-76653600	Weak transcription	Ovary	ovary
44	chr4:76652400-76653800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr4:76652400-76654400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:76652400-76654600	Weak transcription	Small Intestine	intestine
47	chr4:76652400-76654600	Weak transcription	NHDF-Ad	bronchial
48	chr4:76652400-76655000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr4:76652400-76660200	Weak transcription	HSMM	muscle
50	chr4:76652400-76660800	Weak transcription	Stomach Mucosa	stomach

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