Variant report

Variant	rs4371601
Chromosome Location	chr4:152504533-152504534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152497358..152500298-chr4:152502845..152505045,2	K562	blood:

Variant related genes	Relation type
ENSG00000253019	Chromatin interaction

Extended variants
information (count: 144 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs10001439	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs10009423	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs10025109	0.87[EUR][1000 genomes]
rs10031175	0.87[EUR][1000 genomes]
rs10857261	0.89[EUR][1000 genomes]
rs11099813	0.86[EUR][1000 genomes]
rs11099818	0.92[EUR][1000 genomes]
rs11099824	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11556167	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs11723643	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11726171	0.86[EUR][1000 genomes]
rs11726222	0.92[EUR][1000 genomes]
rs11726545	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728541	0.84[EUR][1000 genomes]
rs11729514	0.92[EUR][1000 genomes]
rs11729871	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11730733	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11732441	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs11734176	0.84[EUR][1000 genomes]
rs11735143	0.92[EUR][1000 genomes]
rs11736261	0.84[EUR][1000 genomes]
rs11736961	0.92[EUR][1000 genomes]
rs11934818	0.92[EUR][1000 genomes]
rs11947720	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12054502	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12498556	0.92[EUR][1000 genomes]
rs12498878	0.92[EUR][1000 genomes]
rs12502212	0.92[EUR][1000 genomes]
rs12502967	0.84[EUR][1000 genomes]
rs12504273	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508678	0.92[EUR][1000 genomes]
rs12511280	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1366908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1366910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs1372979	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1443085	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17027716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17027818	0.84[EUR][1000 genomes]
rs17275584	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17275605	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17275612	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17360294	0.89[CEU][hapmap]
rs17360378	0.89[CEU][hapmap]
rs1992517	0.92[EUR][1000 genomes]
rs2406972	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs28417319	0.84[EUR][1000 genomes]
rs28447105	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28463438	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28483174	0.87[EUR][1000 genomes]
rs28498882	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28527216	0.87[EUR][1000 genomes]
rs28545583	0.87[EUR][1000 genomes]
rs28574706	0.87[EUR][1000 genomes]
rs28605105	0.84[EUR][1000 genomes]
rs28608075	0.84[EUR][1000 genomes]
rs28608757	0.84[EUR][1000 genomes]
rs28672085	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28706249	0.84[EUR][1000 genomes]
rs28715753	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3172567	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35588363	0.84[EUR][1000 genomes]
rs36083376	0.92[EUR][1000 genomes]
rs3762906	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs3792689	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3811748	0.84[EUR][1000 genomes]
rs3811749	0.84[EUR][1000 genomes]
rs3934474	0.92[EUR][1000 genomes]
rs4622982	0.90[EUR][1000 genomes]
rs56092201	0.92[EUR][1000 genomes]
rs56199243	0.83[EUR][1000 genomes]
rs56763519	0.89[EUR][1000 genomes]
rs57272881	0.92[EUR][1000 genomes]
rs57348790	0.85[EUR][1000 genomes]
rs57556564	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58443173	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58863309	0.84[EUR][1000 genomes]
rs58961701	0.87[EUR][1000 genomes]
rs59731141	0.92[EUR][1000 genomes]
rs59744221	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59777523	0.84[EUR][1000 genomes]
rs59811197	0.90[EUR][1000 genomes]
rs59984665	0.92[EUR][1000 genomes]
rs60055392	0.84[EUR][1000 genomes]
rs60077220	0.92[EUR][1000 genomes]
rs60122169	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60169090	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60618075	0.88[EUR][1000 genomes]
rs60707008	0.92[EUR][1000 genomes]
rs61294884	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61302767	0.92[EUR][1000 genomes]
rs61630225	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6535802	0.92[EUR][1000 genomes]
rs6535805	0.90[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6813289	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs6817373	0.87[EUR][1000 genomes]
rs6822729	0.87[EUR][1000 genomes]
rs6822737	0.84[EUR][1000 genomes]
rs6826318	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6832899	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6832902	0.84[EUR][1000 genomes]
rs6833277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6835310	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838608	0.90[EUR][1000 genomes]
rs6839738	0.94[EUR][1000 genomes]
rs6841515	0.84[EUR][1000 genomes]
rs6843267	0.87[EUR][1000 genomes]
rs6844169	0.92[EUR][1000 genomes]
rs6845067	0.92[EUR][1000 genomes]
rs6846013	0.92[EUR][1000 genomes]
rs6846759	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6851305	0.84[EUR][1000 genomes]
rs6853342	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856392	0.87[EUR][1000 genomes]
rs6858573	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72962929	0.84[EUR][1000 genomes]
rs73861275	0.84[EUR][1000 genomes]
rs73861826	0.89[EUR][1000 genomes]
rs73861827	0.89[EUR][1000 genomes]
rs73862055	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73862076	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73862080	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73862085	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73864013	0.89[EUR][1000 genomes]
rs7438281	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7653926	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655466	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662214	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7662713	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664074	0.92[EUR][1000 genomes]
rs7671456	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7675933	0.84[EUR][1000 genomes]
rs7677528	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[YRI][hapmap];0.92[EUR][1000 genomes]
rs7684972	0.84[EUR][1000 genomes]
rs7690773	0.84[EUR][1000 genomes]
rs7696468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap]
rs7699787	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9683881	0.86[EUR][1000 genomes]
rs9917912	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9996600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs9999456	0.87[EUR][1000 genomes]

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	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv880624	chr4:152280646-152549112	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv881342	chr4:152363772-152560449	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv830114	chr4:152401288-152548606	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4371601	LRBA	cis	cerebellum	SCAN
rs4371601	SH3D19	cis	cerebellum	SCAN
rs4371601	FAM160A1	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152476600-152526600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:152484800-152518600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:152485600-152509600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:152491200-152519000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:152496600-152526600	Weak transcription	Gastric	stomach
6	chr4:152496800-152530000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:152497200-152505200	Weak transcription	HMEC	breast
8	chr4:152498000-152513600	Weak transcription	Ovary	ovary
9	chr4:152499200-152511800	Weak transcription	Aorta	Aorta
10	chr4:152499200-152521200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:152499200-152567600	Weak transcription	Pancreas	Pancrea
12	chr4:152500000-152511600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:152500200-152505200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:152501800-152504800	Weak transcription	NHEK	skin
15	chr4:152502600-152505600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr4:152503000-152504600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr4:152503400-152504600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:152503800-152504600	Weak transcription	Brain Substantia Nigra	brain
19	chr4:152503800-152505000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:152504200-152504600	Enhancers	Brain Angular Gyrus	brain
21	chr4:152504200-152505400	Enhancers	Fetal Brain Male	brain
22	chr4:152504200-152506400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr4:152504400-152504600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:152504400-152504600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr4:152504400-152506200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links