Variant report

Variant	rs223418
Chromosome Location	chr4:103730493-103730494
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103727572..103730495-chr4:103786922..103788552,2	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10003326	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10012413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs10015289	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap]
rs11097796	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs11722779	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap]
rs11737544	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs12500379	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs12508069	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1383733	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs150893	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap]
rs150895	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs17033381	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap]
rs2086499	0.95[CEU][hapmap];0.89[CHB][hapmap]
rs223308	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223313	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap]
rs223314	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs223315	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs223318	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap]
rs223326	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs223330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs223334	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs223338	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs223339	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs223346	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs223347	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs223349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs223350	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs223353	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs223356	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs223358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs223359	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223363	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs223367	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223381	1.00[CEU][hapmap]
rs223383	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs223385	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs223392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs223395	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs223397	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs223400	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs223401	0.85[JPT][hapmap]
rs223410	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs223412	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs223419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs223420	0.90[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap]
rs223425	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs223438	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs223441	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs223447	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs223448	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs223452	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs223454	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs223457	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs223458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap]
rs223461	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223467	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs223474	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs223475	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs223484	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs223486	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap]
rs223497	0.88[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs223498	0.81[ASW][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap]
rs2866417	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs3774987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs3886722	0.92[CEU][hapmap]
rs3886723	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs3974485	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3974604	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap]
rs3974608	0.92[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap]
rs4623004	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs5028609	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs6419160	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs6533041	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs6533050	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs6533051	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs6533052	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs65671	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]
rs6810668	0.91[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap]
rs6815526	1.00[ASW][hapmap];0.89[LWK][hapmap];0.92[YRI][hapmap]
rs6823625	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs6824070	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap]
rs6846762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs6852141	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap]
rs6853193	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs7254	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap]
rs7663876	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7672319	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap]
rs7676943	0.92[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap]
rs7681629	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap]
rs7685399	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs9307281	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs9999303	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.93[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	nsv594957	chr4:103728010-103870091	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs223418	LRRC37A15P	cis	lung	GTEx
rs223418	CISD2	cis	multi-tissue	Pritchard
rs223418	MANBA	cis	multi-tissue	Pritchard
rs223418	MANBA	cis	parietal	SCAN
rs223418	CISD2	cis	cerebellum	SCAN
rs223418	CISD2	cis	Esophagus Muscularis	GTEx
rs223418	CISD2	cis	Skin Sun Exposed Lower leg	GTEx
rs223418	KRT8P46	cis	lung	GTEx
rs223418	CISD2	cis	parietal	SCAN
rs223418	CISD2	cis	Nerve Tibial	GTEx
rs223418	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs223418	CISD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103700600-103731600	Weak transcription	Pancreas	Pancrea
2	chr4:103707800-103732200	Weak transcription	Right Ventricle	heart
3	chr4:103711200-103731000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:103711200-103731600	Weak transcription	Spleen	Spleen
5	chr4:103711400-103732600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:103712400-103735000	Strong transcription	K562	blood
7	chr4:103712400-103736200	Strong transcription	Fetal Intestine Large	intestine
8	chr4:103712400-103737200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:103712600-103731200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:103712600-103739600	Strong transcription	Fetal Thymus	thymus
11	chr4:103712800-103730600	Strong transcription	Primary B cells from cord blood	blood
12	chr4:103712800-103730800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:103712800-103730800	Strong transcription	NH-A	brain
14	chr4:103712800-103731600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:103712800-103736800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:103713000-103744400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:103713600-103730800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:103714000-103732200	Weak transcription	Esophagus	oesophagus
19	chr4:103714000-103740800	Weak transcription	Aorta	Aorta
20	chr4:103714800-103733200	Strong transcription	Duodenum Mucosa	Duodenum
21	chr4:103714800-103737200	Strong transcription	Dnd41	blood
22	chr4:103715200-103732200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:103715600-103730800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr4:103715600-103731600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:103716000-103731000	Strong transcription	Placenta	Placenta
26	chr4:103716000-103736000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr4:103716200-103730800	Strong transcription	NHEK	skin
28	chr4:103716400-103731200	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr4:103716600-103732200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:103717400-103731400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:103717400-103732200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:103717400-103732200	Weak transcription	Gastric	stomach
33	chr4:103718200-103731200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:103718200-103731200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:103718200-103739200	Weak transcription	Stomach Mucosa	stomach
36	chr4:103718400-103731800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr4:103718400-103732000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr4:103719200-103732000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:103719200-103733200	Weak transcription	Psoas Muscle	Psoas
40	chr4:103719800-103733200	Weak transcription	Small Intestine	intestine
41	chr4:103720000-103732400	Weak transcription	Fetal Brain Male	brain
42	chr4:103723600-103732200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:103723800-103737000	Weak transcription	Colonic Mucosa	Colon
44	chr4:103724400-103732000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr4:103724400-103745800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr4:103724600-103734600	Weak transcription	Fetal Kidney	kidney
47	chr4:103725000-103740600	Weak transcription	Fetal Brain Female	brain
48	chr4:103725400-103730600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:103725600-103734400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr4:103725600-103745000	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links