Variant report

Variant	rs230528
Chromosome Location	chr4:103457585-103457586
allele	A/C
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	chr4:103457385-103458010	GM12878	blood:	n/a	n/a
2	IKZF1	chr4:103457540-103457645	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103452501..103454883-chr4:103456086..103457743,2	K562	blood:
2	chr4:103421947..103425084-chr4:103454080..103458478,5	MCF-7	breast:
3	chr4:103456268..103457811-chr4:103471948..103474293,2	MCF-7	breast:

Variant related genes	Relation type
NFKB1	TF binding region
ENSG00000109320	Chromatin interaction
ENSG00000260651	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1005819	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs1020759	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap]
rs1020760	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs11722146	0.91[JPT][hapmap]
rs11723120	0.90[JPT][hapmap]
rs118882	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs12509517	0.91[JPT][hapmap]
rs1585213	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs1585215	1.00[JPT][hapmap]
rs1598859	0.83[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs1599961	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs17032705	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs170731	1.00[JPT][hapmap]
rs1801	0.91[JPT][hapmap]
rs2168805	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs230491	1.00[JPT][hapmap]
rs230492	1.00[JPT][hapmap]
rs230493	0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs230495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230498	0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs230500	0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs230504	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs230505	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs230509	1.00[JPT][hapmap]
rs230514	1.00[JPT][hapmap]
rs230515	1.00[JPT][hapmap]
rs230516	1.00[JPT][hapmap]
rs230519	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs230520	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs230521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230525	0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs230526	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];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs230529	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs230530	0.85[CHD][hapmap]
rs230531	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs230532	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs230533	1.00[JPT][hapmap]
rs230534	1.00[JPT][hapmap]
rs230535	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs230539	0.95[JPT][hapmap]
rs230540	0.91[JPT][hapmap]
rs230541	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs230542	0.84[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs3755867	0.91[JPT][hapmap]
rs3774933	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3774936	1.00[JPT][hapmap]
rs3774937	0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs3774938	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3774956	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs3774959	0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs3774963	0.90[JPT][hapmap]
rs3774964	0.88[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs3817685	0.95[JPT][hapmap]
rs3821958	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4235404	1.00[JPT][hapmap]
rs4648011	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs4648055	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs4648058	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs4648068	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs4698858	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs4699030	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs747559	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs93059	0.85[CHD][hapmap]
rs9790601	0.91[JPT][hapmap]
rs980455	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1003490	chr4:103391483-103521772	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1004030	chr4:103419352-103504042	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537203	chr4:103419352-103504042	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs230528	MAPKSP1	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103426400-103460800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:103433200-103466000	Weak transcription	Hela-S3	cervix
3	chr4:103440000-103459600	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:103440000-103460600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:103440000-103466200	Weak transcription	Aorta	Aorta
6	chr4:103440000-103484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:103440200-103460600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr4:103440200-103473200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:103440200-103478600	Weak transcription	Right Ventricle	heart
10	chr4:103440200-103488200	Weak transcription	Gastric	stomach
11	chr4:103441400-103464200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:103441400-103469400	Weak transcription	Ovary	ovary
13	chr4:103441400-103482000	Weak transcription	Spleen	Spleen
14	chr4:103442400-103459600	Weak transcription	Fetal Stomach	stomach
15	chr4:103443200-103474200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:103443200-103496000	Weak transcription	A549	lung
17	chr4:103444000-103459600	Weak transcription	Fetal Intestine Small	intestine
18	chr4:103444400-103470600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:103444800-103458600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:103444800-103473000	Weak transcription	Small Intestine	intestine
21	chr4:103445000-103496600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:103445200-103470000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr4:103445600-103460400	Weak transcription	Dnd41	blood
24	chr4:103446200-103459000	Weak transcription	Left Ventricle	heart
25	chr4:103446200-103462800	Weak transcription	Esophagus	oesophagus
26	chr4:103446200-103462800	Weak transcription	Psoas Muscle	Psoas
27	chr4:103446200-103466000	Weak transcription	Lung	lung
28	chr4:103446200-103469200	Weak transcription	Pancreas	Pancrea
29	chr4:103446200-103469800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr4:103446400-103457800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:103446600-103466200	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:103447200-103474000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr4:103449000-103467000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr4:103449200-103460600	Weak transcription	HepG2	liver
35	chr4:103449400-103459000	Weak transcription	Liver	Liver
36	chr4:103449400-103467000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr4:103449600-103460000	Weak transcription	Colonic Mucosa	Colon
38	chr4:103449600-103467800	Weak transcription	Fetal Kidney	kidney
39	chr4:103450200-103460200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr4:103450200-103460600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr4:103450400-103459600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:103450400-103459600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:103450400-103462600	Weak transcription	Fetal Heart	heart
44	chr4:103451600-103462200	Weak transcription	Brain Hippocampus Middle	brain
45	chr4:103451800-103459600	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr4:103452000-103458400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr4:103452000-103459600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr4:103452200-103457600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr4:103452200-103459400	Weak transcription	Fetal Intestine Large	intestine
50	chr4:103454000-103457800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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