Variant report

Variant	rs6677446
Chromosome Location	chr1:173960082-173960083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173959770..173961680-chr1:173990983..173993365,2	K562	blood:
2	chr1:173954538..173956167-chr1:173959585..173961567,2	K562	blood:
3	chr1:173956360..173957903-chr1:173959725..173961914,2	K562	blood:

Variant related genes	Relation type
ENSG00000135870	Chromatin interaction
ENSG00000224977	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13375205	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs58700482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60317356	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60551050	0.89[AFR][1000 genomes]
rs61738616	1.00[EUR][1000 genomes]
rs61826774	0.89[AFR][1000 genomes]
rs61826785	0.85[AFR][1000 genomes]
rs6425263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6425269	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6684527	0.83[ASW][hapmap];0.95[LWK][hapmap];0.85[YRI][hapmap]
rs6686659	1.00[EUR][1000 genomes]
rs7522580	1.00[EUR][1000 genomes]
rs7551109	1.00[EUR][1000 genomes]
rs7554635	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv872550	chr1:173913804-173964206	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv872551	chr1:173913804-174025660	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6677446	NAAA	trans	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173900000-173962400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:173900000-173966600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:173900000-173968200	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr1:173900200-173966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:173900400-173964600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:173900800-173963800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:173901400-173962200	Strong transcription	Duodenum Mucosa	Duodenum
8	chr1:173901600-173966400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:173901600-173966400	Strong transcription	Dnd41	blood
10	chr1:173904000-173966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:173905000-173962400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:173909800-173974200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:173915600-173977800	Weak transcription	Stomach Mucosa	stomach
14	chr1:173923400-173962400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:173929000-173962200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr1:173931200-173962400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:173931200-173962400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:173931200-173965600	Weak transcription	Small Intestine	intestine
19	chr1:173931200-173969800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:173941000-173965000	Strong transcription	Fetal Thymus	thymus
21	chr1:173942200-173967400	Weak transcription	Fetal Heart	heart
22	chr1:173942200-173986200	Weak transcription	Fetal Brain Male	brain
23	chr1:173947000-173966000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:173949200-173970600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:173949600-173965600	Weak transcription	Esophagus	oesophagus
26	chr1:173949600-173970600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:173950200-173961800	Weak transcription	Aorta	Aorta
28	chr1:173950400-173960200	Weak transcription	Brain Angular Gyrus	brain
29	chr1:173950600-173973400	Weak transcription	Psoas Muscle	Psoas
30	chr1:173951400-173960200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:173952200-173967200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:173952800-173960200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:173952800-173960600	Weak transcription	NHEK	skin
34	chr1:173952800-173962200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:173952800-173967600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:173953200-173974200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:173953400-173960200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:173953800-173960200	Weak transcription	Brain Substantia Nigra	brain
39	chr1:173953800-173960400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:173954200-173960200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:173954200-173961000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:173954600-173963600	Strong transcription	Fetal Intestine Large	intestine
43	chr1:173955200-173962600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:173955200-173962800	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr1:173955400-173962200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:173955600-173966200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr1:173956000-173962200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:173956000-173962200	Strong transcription	Brain Germinal Matrix	brain
49	chr1:173956000-173962200	Strong transcription	Fetal Lung	lung
50	chr1:173956200-173960200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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