Variant report

Variant	rs6716262
Chromosome Location	chr2:39968210-39968211
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39962607..39965298-chr2:39967236..39969743,2	K562	blood:
2	chr2:39962720..39965298-chr2:39968180..39969743,3	K562	blood:
3	chr2:39967992..39971094-chr2:39972706..39975248,3	K562	blood:
4	chr2:39955286..39957836-chr2:39966525..39968843,2	K562	blood:
5	chr2:39965935..39968913-chr2:39970630..39974457,4	K562	blood:

Variant related genes	Relation type
ENSG00000138050	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10198734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13388310	1.00[CHB][hapmap]
rs13395966	1.00[EUR][1000 genomes]
rs17024154	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024276	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs17024325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2058621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2110673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2160207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2192712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2540234	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2716706	1.00[EUR][1000 genomes]
rs2716724	0.96[EUR][1000 genomes]
rs2716726	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2716731	0.82[AFR][1000 genomes]
rs2716734	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57481251	0.87[AFR][1000 genomes]
rs57704430	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60003713	1.00[EUR][1000 genomes]
rs6708232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745129	1.00[EUR][1000 genomes]
rs73924911	0.89[AFR][1000 genomes]
rs73924912	0.85[AFR][1000 genomes]
rs73924913	0.89[AFR][1000 genomes]
rs73924914	0.87[AFR][1000 genomes]
rs73924917	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73924918	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73924919	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73924920	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73924934	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7576551	0.88[EUR][1000 genomes]
rs7604790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS 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	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39944400-39976600	Weak transcription	Fetal Brain Male	brain
2	chr2:39957400-39971200	Strong transcription	Primary T cells from cord blood	blood
3	chr2:39959000-39971200	Strong transcription	Fetal Thymus	thymus
4	chr2:39959400-39971000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:39959400-39974200	Strong transcription	Primary B cells from cord blood	blood
6	chr2:39960000-39969000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:39960000-39971000	Strong transcription	K562	blood
8	chr2:39960000-39971200	Strong transcription	Fetal Muscle Trunk	muscle
9	chr2:39960000-39971400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:39960000-39971800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr2:39960200-39971000	Strong transcription	Fetal Muscle Leg	muscle
12	chr2:39960200-39973800	Strong transcription	Primary hematopoietic stem cells	blood
13	chr2:39960200-39987200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:39960400-39970200	Strong transcription	GM12878-XiMat	blood
15	chr2:39960400-39973600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:39960400-39983000	Weak transcription	Stomach Mucosa	stomach
17	chr2:39961200-39974600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:39961400-39969800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:39961400-39984200	Weak transcription	Colonic Mucosa	Colon
20	chr2:39961600-39968800	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:39961600-39971200	Strong transcription	Dnd41	blood
22	chr2:39961800-39971200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr2:39962000-39970600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr2:39962000-39971000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:39962000-39971200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr2:39962200-39970800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:39962200-39971000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr2:39962200-39971200	Strong transcription	Adipose Nuclei	Adipose
29	chr2:39962200-39986800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:39962200-39993200	Strong transcription	Liver	Liver
31	chr2:39962400-39971000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr2:39962600-39970200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:39962600-39971000	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:39962800-39970000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:39962800-39971000	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr2:39962800-39971800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr2:39962800-39980200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr2:39963200-39969800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:39963200-39982000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr2:39963400-39971000	Strong transcription	Ovary	ovary
41	chr2:39964000-39969000	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:39964000-39976800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr2:39964200-39976800	Weak transcription	Brain Substantia Nigra	brain
44	chr2:39964200-39977000	Weak transcription	Brain Angular Gyrus	brain
45	chr2:39964200-39977400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:39964200-39984200	Weak transcription	Psoas Muscle	Psoas
47	chr2:39964400-39977000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr2:39964800-39983000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:39965000-39969000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:39965000-39970800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links