Variant report

Variant	rs65671
Chromosome Location	chr4:103722238-103722239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103721213..103722757-chr4:103748649..103750300,2	MCF-7	breast:
2	chr4:103721670..103724216-chr4:103745688..103748268,3	MCF-7	breast:
3	chr4:103717293..103719590-chr4:103721089..103723107,2	K562	blood:
4	chr4:103719443..103722708-chr4:103736970..103739381,3	K562	blood:

Variant related genes	Relation type
ENSG00000246560	Chromatin interaction
ENSG00000109332	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10003326	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs10012413	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10015289	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs11722779	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11737544	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12500379	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs12508069	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs1383733	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs150893	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs150895	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap]
rs17033381	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223308	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223313	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap]
rs223314	1.00[CEU][hapmap]
rs223315	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap]
rs223318	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223324	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap]
rs223326	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223330	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223334	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap]
rs223338	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223339	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap]
rs223346	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223347	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223349	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223350	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223353	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs223356	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223358	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223359	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223363	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap]
rs223367	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223381	1.00[CEU][hapmap]
rs223383	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap]
rs223385	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223390	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223392	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223395	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs223397	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs223400	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223401	0.91[JPT][hapmap]
rs223410	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap]
rs223412	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs223418	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap]
rs223419	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223420	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap]
rs223425	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223438	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap]
rs223441	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223446	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223447	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap]
rs223448	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223450	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223452	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap]
rs223454	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs223457	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap]
rs223458	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223461	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223467	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs223474	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs223475	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs223484	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap]
rs223486	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs223497	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs223498	0.86[TSI][hapmap]
rs2866417	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3774987	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3886722	0.92[CEU][hapmap]
rs3886723	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs3974485	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs3974604	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs3974608	0.92[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs4623004	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs5028609	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6419160	0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap]
rs6533041	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6533050	0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs6533051	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6533052	0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs6810668	0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs6815526	0.81[ASW][hapmap]
rs6823625	0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs6824070	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6846762	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6852141	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6853193	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7254	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7663876	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7672319	0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs7676943	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs7681629	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs7685399	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs9307281	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs9999303	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs65671	CISD2	cis	parietal	SCAN
rs65671	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs65671	CISD2	cis	Skin Sun Exposed Lower leg	GTEx
rs65671	CISD2	cis	Esophagus Muscularis	GTEx
rs65671	CISD2	cis	Nerve Tibial	GTEx
rs65671	MANBA	cis	multi-tissue	Pritchard
rs65671	KRT8P46	cis	lung	GTEx
rs65671	CISD2	cis	cerebellum	SCAN
rs65671	LRRC37A15P	cis	lung	GTEx
rs65671	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs65671	MANBA	cis	parietal	SCAN
rs65671	CISD2	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 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	chr4:103700600-103731600	Weak transcription	Pancreas	Pancrea
3	chr4:103707800-103724800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:103707800-103732200	Weak transcription	Right Ventricle	heart
5	chr4:103711200-103724800	Weak transcription	Fetal Stomach	stomach
6	chr4:103711200-103731000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:103711200-103731600	Weak transcription	Spleen	Spleen
8	chr4:103711400-103732600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:103711800-103728400	Strong transcription	HSMM	muscle
10	chr4:103712400-103724600	Strong transcription	A549	lung
11	chr4:103712400-103726200	Strong transcription	HSMMtube	muscle
12	chr4:103712400-103726800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr4:103712400-103729200	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr4:103712400-103730000	Strong transcription	Primary hematopoietic stem cells	blood
15	chr4:103712400-103735000	Strong transcription	K562	blood
16	chr4:103712400-103736200	Strong transcription	Fetal Intestine Large	intestine
17	chr4:103712400-103737200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:103712600-103726600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:103712600-103729000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:103712600-103729800	Strong transcription	Adipose Nuclei	Adipose
21	chr4:103712600-103730200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:103712600-103730400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:103712600-103731200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:103712600-103739600	Strong transcription	Fetal Thymus	thymus
25	chr4:103712800-103724800	Weak transcription	Fetal Intestine Small	intestine
26	chr4:103712800-103730600	Strong transcription	Primary B cells from cord blood	blood
27	chr4:103712800-103730800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:103712800-103730800	Strong transcription	NH-A	brain
29	chr4:103712800-103731600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr4:103712800-103736800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:103713000-103744400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:103713600-103727200	Strong transcription	Primary T cells from cord blood	blood
33	chr4:103713600-103730800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:103714000-103725000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr4:103714000-103730400	Strong transcription	GM12878-XiMat	blood
36	chr4:103714000-103732200	Weak transcription	Esophagus	oesophagus
37	chr4:103714000-103740800	Weak transcription	Aorta	Aorta
38	chr4:103714800-103725000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr4:103714800-103726600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr4:103714800-103728200	Strong transcription	Liver	Liver
41	chr4:103714800-103729400	Strong transcription	HUVEC	blood vessel
42	chr4:103714800-103733200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr4:103714800-103737200	Strong transcription	Dnd41	blood
44	chr4:103715000-103724600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr4:103715200-103722400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:103715200-103724800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr4:103715200-103732200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:103715600-103730400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr4:103715600-103730800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr4:103715600-103731600	Strong transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links