Variant report

Variant	rs230535
Chromosome Location	chr4:103448582-103448583
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103447755..103449902-chr4:103466038..103467792,2	K562	blood:
2	chr4:103442159..103444303-chr4:103446884..103449201,2	MCF-7	breast:
3	chr4:103422449..103425804-chr4:103447009..103450716,4	K562	blood:

Variant related genes	Relation type
ENSG00000109320	Chromatin interaction
ENSG00000260651	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1005819	0.91[JPT][hapmap]
rs1020760	0.91[JPT][hapmap]
rs11722146	0.84[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs11723120	0.82[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs118882	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs12509517	0.84[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12648696	0.89[CHB][hapmap]
rs1585213	0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap]
rs1585215	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1598859	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs1599961	0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs1609798	0.80[CEU][hapmap]
rs17032705	0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap]
rs170731	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1801	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2168805	0.95[JPT][hapmap]
rs230491	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230492	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230493	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap]
rs230495	1.00[JPT][hapmap]
rs230496	1.00[JPT][hapmap]
rs230498	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs230500	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs230504	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs230505	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs230509	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230511	0.96[CEU][hapmap]
rs230514	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230515	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230516	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230519	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs230520	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs230521	1.00[JPT][hapmap]
rs230525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs230526	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs230528	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs230529	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs230531	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs230532	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs230533	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230534	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230539	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230540	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230541	0.84[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs230542	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs3755867	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs3774933	1.00[JPT][hapmap]
rs3774936	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3774937	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs3774938	1.00[JPT][hapmap]
rs3774956	0.95[JPT][hapmap]
rs3774959	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs3774963	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3774964	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs3817685	0.95[JPT][hapmap]
rs3821958	0.91[JPT][hapmap]
rs4235404	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4648011	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs4648055	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap]
rs4648058	0.90[JPT][hapmap]
rs4648068	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap]
rs4648133	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs4698858	0.89[JPT][hapmap]
rs4699030	0.84[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs747559	0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs9790601	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs980455	0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs230535	BANK1	cis	parietal	SCAN
rs230535	MANBA	cis	parietal	SCAN
rs230535	RGS20	trans	lymphoblastoid	RTeQTL
rs230535	ADH7	cis	cerebellum	SCAN
rs230535	CISD2	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103425200-103456400	Weak transcription	Osteobl	bone
2	chr4:103426000-103452600	Weak transcription	NH-A	brain
3	chr4:103426000-103456400	Weak transcription	NHDF-Ad	bronchial
4	chr4:103426400-103450000	Weak transcription	HMEC	breast
5	chr4:103426400-103452600	Weak transcription	HSMMtube	muscle
6	chr4:103426400-103460800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr4:103428000-103449200	Weak transcription	Fetal Kidney	kidney
8	chr4:103433200-103466000	Weak transcription	Hela-S3	cervix
9	chr4:103436000-103448600	Weak transcription	HUVEC	blood vessel
10	chr4:103440000-103459600	Weak transcription	Fetal Muscle Leg	muscle
11	chr4:103440000-103460600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:103440000-103466200	Weak transcription	Aorta	Aorta
13	chr4:103440000-103484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:103440200-103451000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:103440200-103460600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr4:103440200-103473200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:103440200-103478600	Weak transcription	Right Ventricle	heart
18	chr4:103440200-103488200	Weak transcription	Gastric	stomach
19	chr4:103441000-103448800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr4:103441200-103448800	Weak transcription	Adipose Nuclei	Adipose
21	chr4:103441400-103464200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr4:103441400-103469400	Weak transcription	Ovary	ovary
23	chr4:103441400-103482000	Weak transcription	Spleen	Spleen
24	chr4:103442400-103459600	Weak transcription	Fetal Stomach	stomach
25	chr4:103443000-103449200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr4:103443000-103455400	Weak transcription	HSMM	muscle
27	chr4:103443200-103449400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr4:103443200-103474200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:103443200-103496000	Weak transcription	A549	lung
30	chr4:103443400-103455400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:103443600-103450000	Weak transcription	NHEK	skin
32	chr4:103443800-103456800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:103444000-103459600	Weak transcription	Fetal Intestine Small	intestine
34	chr4:103444200-103449000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:103444400-103470600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr4:103444600-103448800	Weak transcription	Liver	Liver
37	chr4:103444600-103456000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:103444800-103449000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr4:103444800-103458600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr4:103444800-103473000	Weak transcription	Small Intestine	intestine
41	chr4:103445000-103449000	Weak transcription	Right Atrium	heart
42	chr4:103445000-103449000	Weak transcription	HepG2	liver
43	chr4:103445000-103449200	Weak transcription	Fetal Heart	heart
44	chr4:103445000-103450000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:103445000-103450200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr4:103445000-103496600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:103445200-103448800	Weak transcription	Fetal Lung	lung
48	chr4:103445200-103449200	Weak transcription	Brain Anterior Caudate	brain
49	chr4:103445200-103470000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr4:103445600-103460400	Weak transcription	Dnd41	blood

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