Variant report

Variant	rs9614011
Chromosome Location	chr22:30014581-30014582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30013839..30015515-chr22:30021150..30023734,2	MCF-7	breast:
2	chr22:30013978..30015955-chr22:30016681..30018575,2	K562	blood:
3	chr22:29997853..30001127-chr22:30012116..30016282,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186575	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1058642	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12172347	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12484392	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13054618	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13055568	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13055746	0.97[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13056992	0.81[EUR][1000 genomes]
rs13057041	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800538	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1807506	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2024116	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024119	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024121	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2072301	0.95[CEU][hapmap]
rs2240638	0.95[CEU][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap]
rs2245185	0.87[LWK][hapmap]
rs2267147	0.81[ASN][1000 genomes]
rs2348683	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348684	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530670	0.84[LWK][hapmap]
rs34013089	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3940296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4470427	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67884471	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7287318	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs737975	0.95[CEU][hapmap]
rs737980	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap]
rs8142111	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs867088	0.81[ASN][1000 genomes]
rs9608781	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9608785	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608787	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608789	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608799	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613940	0.83[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs9613942	0.83[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs9613956	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613957	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613961	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9613963	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9613965	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9613970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613977	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613978	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613979	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613980	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9613983	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9613984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613986	0.97[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613990	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613991	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613992	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9613993	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613994	0.97[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613995	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9613996	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613997	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9613998	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9613999	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9614004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9614006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999458	0.82[JPT][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv817417	chr22:29998464-30035142	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9614011	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs9614011	THOC5	cis	Artery Tibial	GTEx
rs9614011	THOC5	cis	Thyroid	GTEx
rs9614011	NIPSNAP1	cis	lymphoblastoid	seeQTL
rs9614011	NF2	cis	parietal	SCAN
rs9614011	NIPSNAP1	cis	parietal	SCAN
rs9614011	THOC5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30000400-30026600	Weak transcription	Gastric	stomach
2	chr22:30001000-30019400	Weak transcription	Thymus	Thymus
3	chr22:30002000-30017600	Weak transcription	Primary T cells from cord blood	blood
4	chr22:30002800-30017600	Weak transcription	Lung	lung
5	chr22:30003000-30016600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr22:30003400-30017200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr22:30003600-30016400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr22:30003800-30032800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr22:30005200-30019400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr22:30005400-30017800	Weak transcription	Primary B cells from cord blood	blood
11	chr22:30006800-30019000	Weak transcription	Fetal Thymus	thymus
12	chr22:30007400-30016800	Weak transcription	Fetal Muscle Leg	muscle
13	chr22:30007600-30017400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr22:30009600-30017600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr22:30011000-30015600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr22:30011000-30017800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr22:30011600-30016800	Weak transcription	Esophagus	oesophagus
18	chr22:30011800-30017000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr22:30011800-30017200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr22:30011800-30026200	Weak transcription	Fetal Stomach	stomach
21	chr22:30013000-30017600	Enhancers	HMEC	breast
22	chr22:30013000-30018400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr22:30013200-30014800	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr22:30013200-30014800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr22:30013200-30015000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr22:30013200-30015000	Enhancers	Hela-S3	cervix
27	chr22:30013200-30015000	Enhancers	HUVEC	blood vessel
28	chr22:30013200-30015200	Enhancers	Muscle Satellite Cultured Cells	--
29	chr22:30013200-30015200	Enhancers	NHDF-Ad	bronchial
30	chr22:30013200-30017200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr22:30013200-30017800	Enhancers	NHLF	lung
32	chr22:30013400-30014800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr22:30013400-30014800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr22:30013400-30014800	Enhancers	Colon Smooth Muscle	Colon
35	chr22:30013400-30014800	Enhancers	Fetal Intestine Small	intestine
36	chr22:30013400-30014800	Enhancers	Rectal Smooth Muscle	rectum
37	chr22:30013400-30014800	Enhancers	Stomach Mucosa	stomach
38	chr22:30013400-30015000	Enhancers	Fetal Heart	heart
39	chr22:30013400-30015000	Enhancers	Fetal Kidney	kidney
40	chr22:30013400-30015000	Enhancers	Fetal Lung	lung
41	chr22:30013400-30015000	Enhancers	HSMM	muscle
42	chr22:30013400-30015000	Enhancers	NH-A	brain
43	chr22:30013400-30017000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr22:30013400-30018000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr22:30013600-30014600	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr22:30013600-30014800	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr22:30013600-30014800	Enhancers	Placenta Amnion	Placenta Amnion
48	chr22:30013600-30015000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr22:30013600-30015000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr22:30013600-30015000	Enhancers	Pancreatic Islets	Pancreatic Islet

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