Variant report

Variant	rs1006867
Chromosome Location	chr7:38410254-38410255
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr7:38409110-38410700	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr7:38410240-38410390	AoAF	blood vessel:	n/a	n/a
3	CTCF	chr7:38410060-38410310	BJ	skin:	n/a	n/a
4	CTCF	chr7:38410140-38410290	AG10803	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38409691..38411244-chr7:38417623..38419459,2	K562	blood:

Variant related genes	Relation type
TRGV1	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1861240	0.92[ASN][1000 genomes]
rs2011898	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2241114	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2534587	0.86[YRI][hapmap]
rs2540188	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2735118	0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2735119	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3778891	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4323384	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4723747	0.92[ASN][1000 genomes]
rs6462834	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6971753	0.92[ASN][1000 genomes]
rs6972066	0.92[ASN][1000 genomes]
rs6972549	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6974770	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7797187	0.95[CHB][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758112	chr7:38218703-38523455	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv2759524	chr7:38218703-38523455	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv427776	chr7:38218703-38523455	Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1025974	chr7:38227528-38503472	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv538819	chr7:38227528-38503472	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv1027803	chr7:38257707-38410660	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv538820	chr7:38257707-38410660	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv1020990	chr7:38257707-38503472	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	nsv820039	chr7:38289515-38411222	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	esv2757222	chr7:38294079-38418165	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv519863	chr7:38318590-38417556	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
13	nsv1019941	chr7:38319437-38472680	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	nsv1031936	chr7:38319437-38503472	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
15	nsv429745	chr7:38323485-38470561	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
16	nsv830965	chr7:38350614-38521047	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
17	nsv1016350	chr7:38378718-38418165	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	esv1850821	chr7:38378932-38411586	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	esv1801754	chr7:38383309-38411786	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
20	esv1801707	chr7:38383509-38411586	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
21	nsv1020630	chr7:38384841-38415389	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
22	nsv1021462	chr7:38384841-38418165	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
23	nsv1032769	chr7:38384841-38418465	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
24	esv1849113	chr7:38387508-38411786	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
25	nsv1034617	chr7:38391353-38415389	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
26	nsv830966	chr7:38393663-38602553	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1006867	VPS41	cis	cerebellum	SCAN
rs1006867	TRGV4	cis	Whole Blood	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38389600-38413800	Weak transcription	K562	blood
2	chr7:38398600-38414600	Weak transcription	Placenta	Placenta
3	chr7:38404400-38410800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr7:38406200-38410600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr7:38406200-38410800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:38407000-38412800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr7:38407200-38411600	Genic enhancers	Primary T cells fromperipheralblood	blood
8	chr7:38407400-38410600	Enhancers	Primary T cells from cord blood	blood
9	chr7:38407600-38410400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr7:38407600-38410400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr7:38407600-38410600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr7:38407600-38412200	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr7:38408000-38411800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr7:38408200-38410400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr7:38408200-38418000	Weak transcription	Pancreas	Pancrea
16	chr7:38408400-38412800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr7:38409400-38410800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:38409600-38410800	Enhancers	Lung	lung
19	chr7:38409600-38412600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:38409600-38412800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:38409600-38412800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:38409600-38412800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:38409600-38423600	Weak transcription	Fetal Kidney	kidney
24	chr7:38409800-38421200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr7:38409800-38438600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr7:38410000-38410800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:38410000-38411000	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr7:38410000-38411800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:38410000-38412000	Weak transcription	Thymus	Thymus
30	chr7:38410000-38412400	Weak transcription	Fetal Muscle Leg	muscle
31	chr7:38410000-38412600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr7:38410000-38412800	Weak transcription	Spleen	Spleen
33	chr7:38410000-38415200	Weak transcription	GM12878-XiMat	blood
34	chr7:38410000-38420800	Strong transcription	Dnd41	blood
35	chr7:38410000-38421800	Weak transcription	Fetal Intestine Small	intestine
36	chr7:38410000-38432800	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr7:38410200-38411800	Strong transcription	Fetal Thymus	thymus
38	chr7:38410200-38412000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr7:38410200-38412200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr7:38410200-38412800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr7:38410200-38414200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr7:38410200-38419800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr7:38410200-38424400	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links