Variant report

Variant	rs9393681
Chromosome Location	chr6:26008260-26008261
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26004960..26009500-chr6:26017429..26023147,9	MCF-7	breast:
2	chr6:25726980..25728872-chr6:26007237..26009757,2	K562	blood:
3	chr6:25992011..25994154-chr6:26005300..26008350,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM38-1	chr6:25998131-26012068	NONHSAT108196

Variant related genes	Relation type
ENSG00000198366	Chromatin interaction
ENSG00000124610	Chromatin interaction
ENSG00000146047	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000272462	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10807006	0.84[AMR][1000 genomes]
rs10807007	1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10946800	0.86[ASN][1000 genomes]
rs1115920	0.86[ASN][1000 genomes]
rs1130000	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1436306	0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs1436309	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1436310	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1541987	0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs1800702	0.84[CEU][hapmap];0.93[YRI][hapmap]
rs1865760	0.86[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs2006736	0.88[CEU][hapmap];0.93[YRI][hapmap]
rs2013063	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2032443	0.84[AMR][1000 genomes]
rs2032445	0.84[AMR][1000 genomes]
rs2032449	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs2032450	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2051544	0.84[CEU][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs2071297	0.86[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs2071298	0.86[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs2071299	0.86[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs2071301	0.86[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs2157050	0.83[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2164485	0.86[ASN][1000 genomes]
rs2164487	0.86[ASN][1000 genomes]
rs2328903	0.89[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs2794719	0.81[CEU][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap]
rs2794720	0.84[CEU][hapmap];0.93[YRI][hapmap]
rs3752419	0.89[CEU][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes]
rs3752420	0.89[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes]
rs3752421	0.86[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs3799371	0.86[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs4478388	0.86[ASN][1000 genomes]
rs4529296	0.84[CEU][hapmap];0.93[YRI][hapmap]
rs6910174	0.86[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs6928717	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6928951	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6929805	0.86[ASN][1000 genomes]
rs6932113	0.86[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs6938083	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6938233	0.86[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs6942196	0.84[CEU][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7450342	0.82[GIH][hapmap]
rs7738854	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7749342	0.82[GIH][hapmap]
rs7753253	0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7766342	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7770139	0.86[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs7772312	0.84[CEU][hapmap];0.84[AMR][1000 genomes]
rs9295679	0.85[ASN][1000 genomes]
rs9295680	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs9295681	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9295684	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9295685	0.81[CEU][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9295687	0.84[CEU][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap]
rs9295688	0.84[CEU][hapmap]
rs9348704	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9348706	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9356991	0.86[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs9358896	0.89[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs9358903	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9358905	0.81[ASN][1000 genomes]
rs9366634	0.84[CEU][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9379814	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9379815	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9379818	0.92[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9379819	1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9379820	0.84[CEU][hapmap];0.84[AMR][1000 genomes]
rs9379821	0.84[AMR][1000 genomes]
rs9379825	0.84[CEU][hapmap]
rs9393677	0.86[ASN][1000 genomes]
rs9393678	0.86[ASN][1000 genomes]
rs9393683	0.88[CEU][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9393684	0.81[ASN][1000 genomes]
rs9461227	0.90[ASN][1000 genomes]
rs9461229	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9461230	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9467641	0.86[ASN][1000 genomes]
rs9467645	0.86[ASN][1000 genomes]
rs9467646	0.89[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs9467647	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9467648	0.86[ASN][1000 genomes]
rs9467650	0.86[ASN][1000 genomes]
rs9467651	0.86[ASN][1000 genomes]
rs9467652	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs9467656	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9467658	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467662	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs9467663	0.88[AMR][1000 genomes]
rs9467672	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv432857	chr6:25957109-26072445	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	451 gene(s)	inside rSNPs	diseases
8	nsv1015627	chr6:25973495-26100483	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
9	nsv538164	chr6:25973495-26100483	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
10	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
11	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
12	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
13	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
14	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9393681	HIST1H3B	cis	cerebellum	SCAN
rs9393681	HIST1H1C	cis	parietal	SCAN
rs9393681	HIST1H2BC	cis	cerebellum	SCAN
rs9393681	TRIM38	cis	Liver	GTEx
rs9393681	U91328.19	cis	Muscle Skeletal	GTEx
rs9393681	HIST1H3H	cis	parietal	SCAN
rs9393681	HIST1H2AA	cis	parietal	SCAN
rs9393681	U91328.19	cis	Adipose Subcutaneous	GTEx
rs9393681	BTN3A2	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25993600-26011200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:25993600-26015800	Weak transcription	Fetal Kidney	kidney
3	chr6:25993600-26016600	Weak transcription	Aorta	Aorta
4	chr6:25993800-26016400	Weak transcription	NHLF	lung
5	chr6:25998600-26008600	Weak transcription	Psoas Muscle	Psoas
6	chr6:25998600-26009200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:25999000-26010000	Weak transcription	Primary B cells from cord blood	blood
8	chr6:25999200-26016400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:25999200-26016600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:25999200-26016600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:25999200-26017200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr6:25999400-26009800	Weak transcription	Gastric	stomach
13	chr6:25999400-26016400	Weak transcription	Right Ventricle	heart
14	chr6:25999400-26016600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:25999400-26016600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:25999400-26016600	Weak transcription	Pancreas	Pancrea
17	chr6:25999400-26017400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:25999600-26008600	Weak transcription	Spleen	Spleen
19	chr6:25999600-26016800	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:25999800-26016600	Weak transcription	Esophagus	oesophagus
21	chr6:26001200-26016800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr6:26001400-26015800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:26001600-26016000	Weak transcription	Liver	Liver
24	chr6:26001600-26016400	Weak transcription	Fetal Intestine Large	intestine
25	chr6:26001600-26017600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:26001600-26020600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:26001800-26008600	Weak transcription	Left Ventricle	heart
28	chr6:26001800-26016400	Weak transcription	Adipose Nuclei	Adipose
29	chr6:26002400-26016400	Weak transcription	Fetal Intestine Small	intestine
30	chr6:26004800-26009400	Weak transcription	HepG2	liver
31	chr6:26004800-26015800	Weak transcription	Fetal Stomach	stomach
32	chr6:26005400-26016400	Weak transcription	Ovary	ovary
33	chr6:26005400-26016600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:26005400-26017200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:26007200-26015600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:26007200-26016000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr6:26007600-26008600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:26007800-26016200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr6:26008000-26010600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:26008200-26008600	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links