Variant report

Variant	rs223498
Chromosome Location	chr4:103651962-103651963
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103651533..103654531-chr4:103655303..103657953,2	K562	blood:
2	chr4:103650888..103653325-chr4:103747345..103748932,2	MCF-7	breast:
3	chr4:103649437..103652154-chr4:103748194..103749901,2	K562	blood:

Variant related genes	Relation type
ENSG00000246560	Chromatin interaction
ENSG00000224207	Chromatin interaction
ENSG00000109332	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs150893	0.86[TSI][hapmap]
rs150895	0.89[TSI][hapmap]
rs17033015	0.80[YRI][hapmap]
rs223313	0.84[TSI][hapmap]
rs223315	0.86[TSI][hapmap]
rs223324	0.81[ASW][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap]
rs223334	0.84[TSI][hapmap]
rs223339	0.84[TSI][hapmap]
rs223353	0.81[ASW][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap]
rs223358	1.00[YRI][hapmap]
rs223363	0.86[TSI][hapmap]
rs223383	0.89[TSI][hapmap]
rs223397	0.89[ASW][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs223410	0.89[ASW][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap]
rs223412	0.89[TSI][hapmap]
rs223418	0.81[ASW][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap]
rs223420	0.89[ASW][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap]
rs223438	0.87[MKK][hapmap];0.89[TSI][hapmap]
rs223447	0.81[ASW][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap]
rs223452	0.81[ASW][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap]
rs223454	0.89[TSI][hapmap]
rs223457	0.89[TSI][hapmap]
rs223461	0.85[JPT][hapmap]
rs223467	0.89[TSI][hapmap]
rs223474	0.81[CEU][hapmap]
rs223475	0.81[CEU][hapmap]
rs223484	0.81[ASW][hapmap];0.81[CEU][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap]
rs223486	0.91[TSI][hapmap]
rs223497	0.89[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs227368	0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs227375	0.89[CEU][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs3974604	0.81[ASW][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap]
rs65671	0.86[TSI][hapmap]
rs6823625	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008110	chr4:103560583-103684526	Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv966303	chr4:103649229-103653443	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs223498	ADH7	cis	cerebellum	SCAN
rs223498	CISD2	cis	cerebellum	SCAN
rs223498	KRT8P46	cis	lung	GTEx
rs223498	CISD2	cis	lymphoblastoid	seeQTL
rs223498	CISD2	cis	Nerve Tibial	GTEx
rs223498	MANBA	cis	multi-tissue	Pritchard
rs223498	CISD2	cis	multi-tissue	Pritchard
rs223498	MANBA	cis	parietal	SCAN
rs223498	CISD2	cis	parietal	SCAN
rs223498	CISD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103547000-103658200	Weak transcription	Small Intestine	intestine
2	chr4:103571800-103655800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:103581800-103681000	Weak transcription	Spleen	Spleen
4	chr4:103609600-103664800	Weak transcription	Esophagus	oesophagus
5	chr4:103618400-103655800	Weak transcription	HSMM	muscle
6	chr4:103627400-103655400	Weak transcription	Lung	lung
7	chr4:103627600-103652400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr4:103630400-103655800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:103632400-103666200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:103632400-103667600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:103634400-103655400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:103634600-103653400	Weak transcription	Fetal Lung	lung
13	chr4:103634600-103655400	Weak transcription	NHDF-Ad	bronchial
14	chr4:103634600-103655600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:103634600-103655600	Weak transcription	NHLF	lung
16	chr4:103634800-103655800	Weak transcription	Osteobl	bone
17	chr4:103636000-103652400	Weak transcription	Colon Smooth Muscle	Colon
18	chr4:103637000-103680800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr4:103638800-103681000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:103639000-103656000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:103639200-103659400	Weak transcription	Ovary	ovary
22	chr4:103639600-103655800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:103641000-103671600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr4:103641200-103652800	Weak transcription	Adipose Nuclei	Adipose
25	chr4:103641200-103653600	Weak transcription	HSMMtube	muscle
26	chr4:103641200-103656200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr4:103641200-103680800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:103641400-103657800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:103641400-103659400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr4:103644400-103655400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr4:103644600-103652200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr4:103644600-103658200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:103644800-103655600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:103644800-103658000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:103644800-103658000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:103645000-103652200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr4:103645000-103653200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr4:103645000-103655200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:103645400-103657200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:103645400-103658200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr4:103647600-103670400	Weak transcription	Liver	Liver
42	chr4:103648800-103655800	Weak transcription	Right Atrium	heart
43	chr4:103649800-103652400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:103650000-103652400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:103650200-103652000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:103650200-103652000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:103650200-103652400	ZNF genes & repeats	Fetal Stomach	stomach
48	chr4:103650200-103658200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr4:103650600-103652400	Strong transcription	Primary T cells from cord blood	blood
50	chr4:103650600-103652400	Strong transcription	Stomach Smooth Muscle	stomach

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