Variant report

Variant	rs6901039
Chromosome Location	chr6:26000885-26000886
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25721531..25723347-chr6:25999446..26002287,2	K562	blood:
2	chr6:25999088..26001646-chr6:26019532..26021139,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM38-1	chr6:25998131-26002137	XLOC_005208
2	lnc-TRIM38-1	chr6:25998131-26002003	ENSG00000272462.2
3	lnc-TRIM38-1	chr6:25998131-26012068	NONHSAT108196

Variant related genes	Relation type
ENSG00000198366	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10425	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs115810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1165201	0.87[CHD][hapmap]
rs12346	0.87[CEU][hapmap];0.96[CHD][hapmap];0.81[TSI][hapmap]
rs129129	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1540275	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1540276	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs169219	0.86[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap]
rs175319	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1935235	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs198810	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs198815	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs198820	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs198845	0.86[CHB][hapmap];0.96[CHD][hapmap]
rs198848	0.86[CHB][hapmap];0.96[CHD][hapmap]
rs198852	0.86[CHB][hapmap];0.96[CHD][hapmap]
rs198853	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.82[TSI][hapmap]
rs199725	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs199726	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs199734	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs199736	0.81[ASN][1000 genomes]
rs199737	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs199739	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs199741	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs199750	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs199751	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs199752	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs199753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199754	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs199755	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2032447	0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2051540	0.81[ASN][1000 genomes]
rs2213284	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2230655	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34413295	0.88[ASN][1000 genomes]
rs3752416	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs428469	1.00[CHB][hapmap]
rs4401650	0.88[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs442601	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs531750	0.86[CHB][hapmap]
rs537581	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs599444	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs645279	0.86[CHB][hapmap]
rs6922788	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6942072	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7756117	0.88[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7760848	0.83[ASN][1000 genomes]
rs807205	0.83[ASN][1000 genomes]
rs807212	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs807214	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9356995	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356996	0.81[ASN][1000 genomes]
rs9358901	0.88[CEU][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9379811	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9467664	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	esv3396495	chr6:26000603-26000905	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6901039	HIST1H2AJ	cis	parietal	SCAN
rs6901039	HIST1H2AA	cis	parietal	SCAN
rs6901039	ZNF187	cis	parietal	SCAN
rs6901039	HIST1H2BB	cis	parietal	SCAN
rs6901039	HIST1H2BD	cis	multi-tissue	Pritchard
rs6901039	HIST1H4I	cis	cerebellum	SCAN
rs6901039	ZNF184	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25993400-26001000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:25993400-26001200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:25993400-26004200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:25993400-26007400	Weak transcription	Small Intestine	intestine
5	chr6:25993600-26001000	Weak transcription	Brain Anterior Caudate	brain
6	chr6:25993600-26003000	Weak transcription	Thymus	Thymus
7	chr6:25993600-26003400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:25993600-26005800	Weak transcription	HSMM	muscle
9	chr6:25993600-26005800	Weak transcription	HSMMtube	muscle
10	chr6:25993600-26006000	Weak transcription	Brain Substantia Nigra	brain
11	chr6:25993600-26006400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:25993600-26007400	Weak transcription	Brain Angular Gyrus	brain
13	chr6:25993600-26011200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:25993600-26015800	Weak transcription	Fetal Kidney	kidney
15	chr6:25993600-26016600	Weak transcription	Aorta	Aorta
16	chr6:25993800-26003400	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:25993800-26016400	Weak transcription	NHLF	lung
18	chr6:25994000-26003600	Weak transcription	Placenta	Placenta
19	chr6:25994000-26006400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:25994000-26006400	Weak transcription	HUVEC	blood vessel
21	chr6:25994200-26006400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:25994400-26003600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr6:25997800-26001800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr6:25997800-26002400	Strong transcription	Fetal Intestine Small	intestine
25	chr6:25997800-26006400	Weak transcription	K562	blood
26	chr6:25998000-26001600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:25998000-26001800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:25998000-26001800	Strong transcription	Stomach Smooth Muscle	stomach
29	chr6:25998400-26002200	Weak transcription	GM12878-XiMat	blood
30	chr6:25998600-26008600	Weak transcription	Psoas Muscle	Psoas
31	chr6:25998600-26009200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:25998800-26001000	Weak transcription	A549	lung
33	chr6:25999000-26001400	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr6:25999000-26001400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:25999000-26006800	Weak transcription	Primary T cells from cord blood	blood
36	chr6:25999000-26007800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr6:25999000-26010000	Weak transcription	Primary B cells from cord blood	blood
38	chr6:25999200-26001400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr6:25999200-26003000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:25999200-26003600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:25999200-26006400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:25999200-26006400	Weak transcription	Lung	lung
43	chr6:25999200-26007400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:25999200-26016400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:25999200-26016600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr6:25999200-26016600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr6:25999200-26017200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr6:25999400-26001000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:25999400-26001000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:25999400-26001200	Weak transcription	Fetal Stomach	stomach

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