Variant report

Variant	rs223446
Chromosome Location	chr4:103714182-103714183
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103711113..103714481-chr4:103747223..103749137,4	MCF-7	breast:
2	chr4:103713400..103715221-chr4:103814511..103816662,2	K562	blood:
3	chr4:103711798..103714550-chr4:103718145..103720751,3	K562	blood:
4	chr4:103713070..103714725-chr4:103740099..103742111,2	K562	blood:
5	chr4:103711798..103714749-chr4:103718145..103719844,2	K562	blood:

Variant related genes	Relation type
ENSG00000109332	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10003326	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs10012413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10015289	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs11722779	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs11737544	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs12500379	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs12508069	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap]
rs150893	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs150895	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17033381	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap]
rs223308	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223313	0.87[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs223314	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs223315	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223318	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223334	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223338	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs223339	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223346	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223347	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223350	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs223353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223359	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223363	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223367	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223381	1.00[CEU][hapmap]
rs223383	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223385	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223395	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223397	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs223401	0.91[JPT][hapmap]
rs223410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs223412	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs223419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223420	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs223425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223441	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223448	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223454	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223457	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs223461	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223467	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223474	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223475	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223484	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223486	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs223497	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3774987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3886722	0.92[CEU][hapmap]
rs3886723	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs3974604	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs3974608	0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs5028609	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6419160	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs6533041	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6533050	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6533051	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6533052	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs65671	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6810668	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap]
rs6815526	1.00[YRI][hapmap]
rs6823625	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6824070	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs6846762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6852141	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs7254	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7663876	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7672319	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7676943	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7681629	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap]
rs7685399	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs9307281	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs9999303	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526256	chr4:103712589-103728010	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs223446	CISD2	cis	multi-tissue	Pritchard
rs223446	CISD2	cis	Nerve Tibial	GTEx
rs223446	MANBA	cis	multi-tissue	Pritchard
rs223446	KRT8P46	cis	lung	GTEx
rs223446	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs223446	LRRC37A15P	cis	lung	GTEx
rs223446	CISD2	cis	Esophagus Muscularis	GTEx
rs223446	CISD2	cis	Skin Sun Exposed Lower leg	GTEx
rs223446	CISD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103699400-103725000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:103700000-103714800	Weak transcription	Fetal Heart	heart
3	chr4:103700200-103716800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr4:103700400-103716200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:103700600-103716000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:103700600-103731600	Weak transcription	Pancreas	Pancrea
7	chr4:103701000-103714800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr4:103701400-103718000	Weak transcription	Lung	lung
9	chr4:103702200-103716200	Weak transcription	NHEK	skin
10	chr4:103702200-103719000	Weak transcription	Small Intestine	intestine
11	chr4:103702800-103717000	Weak transcription	Fetal Brain Male	brain
12	chr4:103703400-103714800	Weak transcription	HepG2	liver
13	chr4:103704800-103716000	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:103706400-103716200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:103706400-103719000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:103707800-103716000	Weak transcription	Psoas Muscle	Psoas
17	chr4:103707800-103724800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:103707800-103732200	Weak transcription	Right Ventricle	heart
19	chr4:103710400-103718800	Weak transcription	Thymus	Thymus
20	chr4:103710600-103715000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr4:103710600-103717000	Weak transcription	Hela-S3	cervix
22	chr4:103710800-103719600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:103711000-103716000	Weak transcription	Placenta	Placenta
24	chr4:103711000-103716800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:103711000-103717800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:103711200-103716200	Weak transcription	Brain Anterior Caudate	brain
27	chr4:103711200-103716200	Weak transcription	Fetal Lung	lung
28	chr4:103711200-103717000	Weak transcription	Fetal Kidney	kidney
29	chr4:103711200-103724800	Weak transcription	Fetal Stomach	stomach
30	chr4:103711200-103731000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:103711200-103731600	Weak transcription	Spleen	Spleen
32	chr4:103711400-103714600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:103711400-103714800	Weak transcription	HUVEC	blood vessel
34	chr4:103711400-103715800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr4:103711400-103716000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr4:103711400-103716000	Weak transcription	Brain Substantia Nigra	brain
37	chr4:103711400-103732600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr4:103711600-103714800	Weak transcription	Dnd41	blood
39	chr4:103711600-103719000	Weak transcription	Brain Germinal Matrix	brain
40	chr4:103711800-103715000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr4:103711800-103715800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:103711800-103716200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr4:103711800-103728400	Strong transcription	HSMM	muscle
44	chr4:103712000-103715200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr4:103712000-103715600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr4:103712200-103719600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:103712400-103714200	Strong transcription	Fetal Muscle Leg	muscle
48	chr4:103712400-103714200	Strong transcription	Left Ventricle	heart
49	chr4:103712400-103715200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:103712400-103716200	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links