Variant report

Variant	rs6998446
Chromosome Location	chr8:61193150-61193151
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:61191831..61193372-chr8:61284634..61287151,2	K562	blood:
2	chr8:61142783..61148206-chr8:61191539..61194824,4	K562	blood:
3	chr8:61153089..61155024-chr8:61191912..61193878,2	K562	blood:
4	chr8:61188816..61193463-chr8:61245871..61250410,5	K562	blood:
5	chr8:61191754..61193804-chr8:61209326..61211666,3	K562	blood:

Variant related genes	Relation type
ENSG00000178538	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10086341	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10093008	0.91[AFR][1000 genomes]
rs10097537	0.91[AFR][1000 genomes]
rs10101374	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10957128	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11774698	0.88[AFR][1000 genomes]
rs11774872	0.90[AFR][1000 genomes]
rs11781514	0.88[AFR][1000 genomes]
rs11994317	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13266513	0.87[AFR][1000 genomes]
rs13267008	0.91[AFR][1000 genomes]
rs13269948	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13272076	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1480339	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1824999	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1904780	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4737556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6471856	0.87[AFR][1000 genomes]
rs6471857	0.92[ASW][hapmap];0.96[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs6471858	0.92[ASW][hapmap];0.96[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs6471859	0.91[AFR][1000 genomes]
rs6471860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6983830	0.91[AFR][1000 genomes]
rs7001157	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7002077	0.82[AFR][1000 genomes]
rs7002369	0.92[ASW][hapmap];0.96[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7002846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7002871	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7004004	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7463930	0.90[AFR][1000 genomes]
rs7463939	0.91[AFR][1000 genomes]
rs7464181	0.93[AFR][1000 genomes]
rs7464531	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7813357	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7825247	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7826329	0.90[AFR][1000 genomes]
rs7832419	0.91[AFR][1000 genomes]
rs7840279	0.91[AFR][1000 genomes]
rs7841396	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7845524	0.91[AFR][1000 genomes]
rs8180936	0.87[YRI][hapmap]
rs9643367	0.87[YRI][hapmap]
rs9643368	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1022752	chr8:61095248-61322302	Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv831333	chr8:61102862-61275122	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv3371465	chr8:61115030-61356658	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv890943	chr8:61134995-61225652	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv831334	chr8:61148796-61330190	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6998446	CA8	cis	lung	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61167000-61193200	Weak transcription	Gastric	stomach
2	chr8:61167000-61193200	Weak transcription	Lung	lung
3	chr8:61167000-61193200	Weak transcription	Pancreas	Pancrea
4	chr8:61187800-61193200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr8:61191800-61193400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr8:61191800-61194400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr8:61192200-61193200	Active TSS	Right Ventricle	heart
8	chr8:61192200-61194600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr8:61192200-61194800	Active TSS	Right Atrium	heart
10	chr8:61192400-61194200	Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr8:61192400-61194200	Active TSS	A549	lung
12	chr8:61192400-61194600	Active TSS	K562	blood
13	chr8:61192600-61194400	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr8:61192600-61194600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr8:61192800-61194200	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr8:61192800-61194400	Bivalent/Poised TSS	Fetal Brain Female	brain
17	chr8:61192800-61194600	Bivalent/Poised TSS	Fetal Stomach	stomach
18	chr8:61193000-61193200	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr8:61193000-61193200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
20	chr8:61193000-61193200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr8:61193000-61193200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
22	chr8:61193000-61193200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
23	chr8:61193000-61193200	Active TSS	Adipose Nuclei	Adipose
24	chr8:61193000-61193200	Active TSS	Brain Angular Gyrus	brain
25	chr8:61193000-61193200	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr8:61193000-61193200	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr8:61193000-61193200	Active TSS	Brain Substantia Nigra	brain
28	chr8:61193000-61193200	Active TSS	Colonic Mucosa	Colon
29	chr8:61193000-61193200	Active TSS	Duodenum Mucosa	Duodenum
30	chr8:61193000-61193200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr8:61193000-61193200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
32	chr8:61193000-61193200	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
33	chr8:61193000-61193200	Active TSS	Placenta	Placenta
34	chr8:61193000-61193200	Active TSS	Fetal Thymus	thymus
35	chr8:61193000-61193200	Active TSS	Rectal Smooth Muscle	rectum
36	chr8:61193000-61193200	Enhancers	Spleen	Spleen
37	chr8:61193000-61193200	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
38	chr8:61193000-61193400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
39	chr8:61193000-61193400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr8:61193000-61193400	Bivalent Enhancer	Liver	Liver
41	chr8:61193000-61193600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
42	chr8:61193000-61193800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr8:61193000-61193800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr8:61193000-61194000	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr8:61193000-61194000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr8:61193000-61194000	Bivalent/Poised TSS	Left Ventricle	heart
47	chr8:61193000-61194400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
48	chr8:61193000-61194400	Active TSS	Primary T cells from cord blood	blood
49	chr8:61193000-61194400	Active TSS	Brain Cingulate Gyrus	brain
50	chr8:61193000-61194400	Active TSS	Rectal Mucosa Donor 31	rectum

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