Variant report

Variant	rs230530
Chromosome Location	chr4:103453980-103453981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103418457..103421752-chr4:103450464..103454174,4	MCF-7	breast:
2	chr4:103440956..103442582-chr4:103451787..103454591,2	MCF-7	breast:
3	chr4:103452501..103454883-chr4:103456086..103457743,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1054029	0.82[JPT][hapmap]
rs1585214	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1598856	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs17033015	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs179195	0.81[JPT][hapmap]
rs227361	0.81[JPT][hapmap]
rs228614	0.81[JPT][hapmap]
rs228617	0.81[JPT][hapmap]
rs228619	0.81[JPT][hapmap]
rs230505	0.85[CHD][hapmap]
rs230510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs230526	0.84[CHD][hapmap]
rs230528	0.85[CHD][hapmap]
rs230529	0.85[CHD][hapmap]
rs3774932	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3774968	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs434644	0.85[JPT][hapmap]
rs4648011	0.84[CHD][hapmap]
rs93059	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs230530	CISD2	cis	cerebellum	SCAN
rs230530	RG9MTD2	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103425200-103456400	Weak transcription	Osteobl	bone
2	chr4:103426000-103456400	Weak transcription	NHDF-Ad	bronchial
3	chr4:103426400-103460800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:103433200-103466000	Weak transcription	Hela-S3	cervix
5	chr4:103440000-103459600	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:103440000-103460600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:103440000-103466200	Weak transcription	Aorta	Aorta
8	chr4:103440000-103484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:103440200-103460600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:103440200-103473200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:103440200-103478600	Weak transcription	Right Ventricle	heart
12	chr4:103440200-103488200	Weak transcription	Gastric	stomach
13	chr4:103441400-103464200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:103441400-103469400	Weak transcription	Ovary	ovary
15	chr4:103441400-103482000	Weak transcription	Spleen	Spleen
16	chr4:103442400-103459600	Weak transcription	Fetal Stomach	stomach
17	chr4:103443000-103455400	Weak transcription	HSMM	muscle
18	chr4:103443200-103474200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:103443200-103496000	Weak transcription	A549	lung
20	chr4:103443400-103455400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:103443800-103456800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:103444000-103459600	Weak transcription	Fetal Intestine Small	intestine
23	chr4:103444400-103470600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:103444600-103456000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:103444800-103458600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr4:103444800-103473000	Weak transcription	Small Intestine	intestine
27	chr4:103445000-103496600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:103445200-103470000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr4:103445600-103460400	Weak transcription	Dnd41	blood
30	chr4:103446000-103456200	Strong transcription	Primary B cells from cord blood	blood
31	chr4:103446200-103455200	Weak transcription	Placenta	Placenta
32	chr4:103446200-103459000	Weak transcription	Left Ventricle	heart
33	chr4:103446200-103462800	Weak transcription	Esophagus	oesophagus
34	chr4:103446200-103462800	Weak transcription	Psoas Muscle	Psoas
35	chr4:103446200-103466000	Weak transcription	Lung	lung
36	chr4:103446200-103469200	Weak transcription	Pancreas	Pancrea
37	chr4:103446200-103469800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:103446400-103457800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:103446600-103455200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:103446600-103466200	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:103447200-103474000	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr4:103449000-103467000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr4:103449200-103455800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr4:103449200-103456800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:103449200-103460600	Weak transcription	HepG2	liver
46	chr4:103449400-103459000	Weak transcription	Liver	Liver
47	chr4:103449400-103467000	Strong transcription	Primary B cells from peripheral blood	blood
48	chr4:103449600-103454000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr4:103449600-103456200	Weak transcription	Brain Anterior Caudate	brain
50	chr4:103449600-103460000	Weak transcription	Colonic Mucosa	Colon

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