Variant report

Variant	rs11971500
Chromosome Location	chr7:6271994-6271995
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:6266989..6268669-chr7:6270882..6273016,2	K562	blood:
2	chr7:6269538..6272239-chr7:6272463..6274573,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11974287	1.00[AMR][1000 genomes]
rs11980833	1.00[AMR][1000 genomes]
rs13309885	1.00[AMR][1000 genomes]
rs17136039	1.00[AMR][1000 genomes]
rs35448997	1.00[AMR][1000 genomes]
rs60874263	1.00[AMR][1000 genomes]
rs61446642	1.00[AMR][1000 genomes]
rs6463536	0.89[YRI][hapmap]
rs6951753	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs6957141	0.86[ASW][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs6957720	1.00[AMR][1000 genomes]
rs6957737	1.00[AMR][1000 genomes]
rs6970518	1.00[AMR][1000 genomes]
rs7781006	0.86[ASW][hapmap];0.89[YRI][hapmap];1.00[AMR][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	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
2	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
3	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
5	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
7	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
8	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv530989	chr7:6176729-6438197	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv482829	chr7:6231809-6407606	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1032987	chr7:6246313-6373054	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv538714	chr7:6246313-6373054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11971500	C5orf55	trans	lymphoblastoid	seeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6259400-6276800	Weak transcription	Aorta	Aorta
2	chr7:6267800-6274400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr7:6268000-6272000	Weak transcription	Colonic Mucosa	Colon
4	chr7:6268200-6272000	Weak transcription	Brain Substantia Nigra	brain
5	chr7:6268400-6272000	Weak transcription	Fetal Intestine Small	intestine
6	chr7:6268400-6273400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:6268400-6273800	Weak transcription	Fetal Thymus	thymus
8	chr7:6268400-6274000	Weak transcription	Thymus	Thymus
9	chr7:6268600-6272000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr7:6268800-6272000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr7:6268800-6272000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr7:6268800-6272000	Weak transcription	Small Intestine	intestine
13	chr7:6268800-6272200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr7:6268800-6272200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr7:6268800-6272400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:6268800-6272400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr7:6268800-6272800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr7:6268800-6273000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:6268800-6274000	Weak transcription	Primary T cells from cord blood	blood
20	chr7:6268800-6282400	Weak transcription	HMEC	breast
21	chr7:6268800-6285000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr7:6269000-6272000	Weak transcription	HSMM	muscle
23	chr7:6269000-6272000	Weak transcription	Osteobl	bone
24	chr7:6269200-6272000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr7:6269200-6272000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr7:6269200-6272000	Weak transcription	GM12878-XiMat	blood
27	chr7:6269200-6272000	Weak transcription	HSMMtube	muscle
28	chr7:6269200-6272000	Weak transcription	NHDF-Ad	bronchial
29	chr7:6269200-6272200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:6269200-6274000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr7:6269200-6275000	Weak transcription	Fetal Lung	lung
32	chr7:6269200-6275400	Weak transcription	Fetal Heart	heart
33	chr7:6269200-6288000	Weak transcription	NHEK	skin
34	chr7:6269600-6272400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:6269600-6275400	Weak transcription	Fetal Kidney	kidney
36	chr7:6269600-6276600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:6269800-6272400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr7:6270000-6272000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:6270000-6272000	Weak transcription	Fetal Stomach	stomach
40	chr7:6270000-6272000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr7:6270200-6272000	Enhancers	Adipose Nuclei	Adipose
42	chr7:6270200-6273000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr7:6270400-6272800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr7:6270400-6275000	Enhancers	Left Ventricle	heart
45	chr7:6270600-6273000	Enhancers	Right Atrium	heart
46	chr7:6270600-6275000	Enhancers	Lung	lung
47	chr7:6270600-6275000	Enhancers	Psoas Muscle	Psoas
48	chr7:6270600-6275000	Enhancers	Right Ventricle	heart
49	chr7:6270800-6272200	Enhancers	Primary T cells fromperipheralblood	blood
50	chr7:6270800-6273000	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links