Variant report

Variant	rs34613987
Chromosome Location	chr6:27433029-27433030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27387983..27390252-chr6:27430155..27433045,2	K562	blood:
2	chr6:27431405..27433354-chr6:27435095..27436634,2	K562	blood:
3	chr6:27417775..27420276-chr6:27432383..27434264,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10484399	0.87[EUR][1000 genomes]
rs13191227	0.80[EUR][1000 genomes]
rs13191474	0.87[EUR][1000 genomes]
rs13195040	0.87[EUR][1000 genomes]
rs13195636	0.89[EUR][1000 genomes]
rs13196692	0.80[EUR][1000 genomes]
rs13202775	0.82[EUR][1000 genomes]
rs13207689	0.82[EUR][1000 genomes]
rs13209332	0.89[EUR][1000 genomes]
rs13218537	0.80[EUR][1000 genomes]
rs34105070	0.82[EUR][1000 genomes]
rs34196306	0.87[EUR][1000 genomes]
rs34332556	0.80[EUR][1000 genomes]
rs34573979	0.93[EUR][1000 genomes]
rs34864796	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34953377	0.80[EUR][1000 genomes]
rs34965299	0.89[EUR][1000 genomes]
rs35120058	0.80[EUR][1000 genomes]
rs35848276	0.89[EUR][1000 genomes]
rs41269265	0.87[EUR][1000 genomes]
rs58616630	0.93[EUR][1000 genomes]
rs66785117	0.89[EUR][1000 genomes]
rs66841633	0.80[EUR][1000 genomes]
rs67240003	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67859638	0.82[EUR][1000 genomes]
rs6904596	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6918792	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7749305	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
3	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34613987	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs34613987	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs34613987	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27412600-27438000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:27415400-27438600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:27415800-27434000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr6:27424000-27439800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:27425000-27438800	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:27425200-27433800	Weak transcription	Psoas Muscle	Psoas
7	chr6:27425200-27435000	Weak transcription	Right Ventricle	heart
8	chr6:27425400-27435200	Weak transcription	Brain Substantia Nigra	brain
9	chr6:27425400-27438400	Weak transcription	Fetal Brain Male	brain
10	chr6:27425600-27439400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:27426400-27438200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
12	chr6:27426600-27438200	Strong transcription	Fetal Thymus	thymus
13	chr6:27427800-27440000	Weak transcription	Esophagus	oesophagus
14	chr6:27428200-27433600	ZNF genes & repeats	Fetal Intestine Large	intestine
15	chr6:27428400-27434800	Weak transcription	HUVEC	blood vessel
16	chr6:27428400-27438800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:27428800-27434800	Weak transcription	Gastric	stomach
18	chr6:27428800-27437800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:27428800-27439800	Weak transcription	Pancreas	Pancrea
20	chr6:27429000-27433400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:27429000-27433600	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:27429000-27433800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:27429000-27433800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:27429000-27434600	Weak transcription	NHEK	skin
25	chr6:27429000-27435000	Weak transcription	Aorta	Aorta
26	chr6:27429000-27435200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:27429200-27433400	Weak transcription	Placenta	Placenta
28	chr6:27429200-27435000	Strong transcription	Thymus	Thymus
29	chr6:27429200-27437400	Weak transcription	Small Intestine	intestine
30	chr6:27429400-27433400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:27429400-27433600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:27429400-27434400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr6:27429400-27434800	Weak transcription	Spleen	Spleen
34	chr6:27429400-27437200	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr6:27429400-27439000	Weak transcription	Stomach Mucosa	stomach
36	chr6:27429600-27434800	Weak transcription	Ovary	ovary
37	chr6:27429600-27435000	Weak transcription	Lung	lung
38	chr6:27429600-27437800	Weak transcription	Fetal Heart	heart
39	chr6:27429600-27439800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:27429600-27440000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:27429600-27440000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr6:27429800-27433400	Weak transcription	Osteobl	bone
43	chr6:27429800-27433600	Weak transcription	Brain Anterior Caudate	brain
44	chr6:27429800-27433600	Weak transcription	Fetal Brain Female	brain
45	chr6:27429800-27433800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr6:27429800-27434200	Weak transcription	Adipose Nuclei	Adipose
47	chr6:27429800-27434400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr6:27429800-27434600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr6:27429800-27435400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr6:27429800-27436200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links