Variant report

Variant	rs17023901
Chromosome Location	chr2:100907128-100907129
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:99952367..99954549-chr2:100906895..100909428,2	K562	blood:
2	chr2:100907128..100908845-chr2:101037649..101040314,2	MCF-7	breast:
3	chr2:100887822..100891668-chr2:100905183..100909067,4	MCF-7	breast:
4	chr2:100898914..100902025-chr2:100905240..100908498,4	K562	blood:
5	chr2:100882860..100889379-chr2:100906197..100910186,11	MCF-7	breast:
6	chr2:100887980..100890347-chr2:100906577..100908691,2	K562	blood:
7	chr2:100906831..100909358-chr2:100926038..100929328,3	MCF-7	breast:
8	chr2:100889401..100893026-chr2:100904259..100909793,5	MCF-7	breast:
9	chr2:100900693..100917248-chr2:100932005..100942326,51	MCF-7	breast:
10	chr2:100906911..100909075-chr2:101026496..101029080,2	MCF-7	breast:
11	chr2:100879379..100882180-chr2:100906907..100909582,4	MCF-7	breast:
12	chr2:100906645..100910351-chr2:100915314..100919031,3	K562	blood:
13	chr2:100907126..100910810-chr2:100936315..100940527,7	K562	blood:
14	chr2:100906194..100908504-chr2:101178325..101181270,2	MCF-7	breast:
15	chr2:100906230..100908790-chr2:100951574..100954485,3	MCF-7	breast:
16	chr2:100899904..100902049-chr2:100905523..100907621,2	MCF-7	breast:
17	chr2:100875966..100878799-chr2:100906876..100908974,2	MCF-7	breast:
18	chr2:100883299..100887347-chr2:100906337..100908618,4	MCF-7	breast:
19	chr2:100891457..100894388-chr2:100906302..100910364,4	K562	blood:
20	chr2:100906194..100910090-chr2:100935878..100940937,6	K562	blood:
21	chr2:100893081..100895089-chr2:100906389..100909363,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000158417	Chromatin interaction
ENSG00000170500	Chromatin interaction
ENSG00000115514	Chromatin interaction
ENSG00000115539	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10174820	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10176062	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10176143	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10195018	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10201565	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10201669	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11123822	0.80[ASN][1000 genomes]
rs11890655	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11902303	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12615454	0.81[JPT][hapmap]
rs13391517	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13400045	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409545	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3748928	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4850925	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851279	0.81[JPT][hapmap]
rs55759234	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6542922	0.81[JPT][hapmap]
rs6542925	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7556910	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs764828	0.82[JPT][hapmap];0.80[ASN][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	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS 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	30 gene(s)	inside rSNPs	diseases
3	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100891800-100907600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:100892200-100909800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:100896600-100907600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:100898400-100908200	Weak transcription	Fetal Lung	lung
5	chr2:100898400-100915600	Weak transcription	Right Atrium	heart
6	chr2:100898800-100915000	Weak transcription	Adipose Nuclei	Adipose
7	chr2:100899000-100907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:100900200-100919000	Strong transcription	Fetal Brain Female	brain
9	chr2:100900800-100907800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:100900800-100926600	Weak transcription	Right Ventricle	heart
11	chr2:100901000-100937000	Weak transcription	Fetal Brain Male	brain
12	chr2:100901600-100907200	Strong transcription	Brain Inferior Temporal Lobe	brain
13	chr2:100902400-100907400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:100902400-100908000	Strong transcription	Stomach Smooth Muscle	stomach
15	chr2:100902600-100907400	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:100902600-100907600	Weak transcription	Fetal Stomach	stomach
17	chr2:100903000-100907200	Weak transcription	Esophagus	oesophagus
18	chr2:100903000-100907600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:100903200-100907200	Weak transcription	HUVEC	blood vessel
20	chr2:100903200-100907400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:100903200-100918000	Weak transcription	Liver	Liver
22	chr2:100903400-100907200	Weak transcription	Fetal Intestine Small	intestine
23	chr2:100903400-100907400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:100903400-100907600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:100903400-100907600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:100903400-100909400	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:100903400-100930800	Weak transcription	Brain Substantia Nigra	brain
28	chr2:100903600-100907800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr2:100903600-100907800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:100903600-100907800	Weak transcription	Brain Anterior Caudate	brain
31	chr2:100903600-100908200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:100903600-100914400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:100903600-100926200	Weak transcription	Fetal Kidney	kidney
34	chr2:100903800-100907800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:100904000-100907200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr2:100904200-100907400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:100904800-100907800	Weak transcription	Gastric	stomach
38	chr2:100905400-100907200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:100905600-100907200	Strong transcription	Left Ventricle	heart
40	chr2:100905600-100907200	Genic enhancers	K562	blood
41	chr2:100905600-100907400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr2:100906200-100907400	Strong transcription	Brain Angular Gyrus	brain
43	chr2:100906400-100907200	Enhancers	Dnd41	blood
44	chr2:100906400-100907400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:100906400-100909200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:100906600-100907200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:100906600-100907600	Enhancers	Hela-S3	cervix
48	chr2:100906600-100911400	Strong transcription	Brain Germinal Matrix	brain
49	chr2:100906800-100907400	Enhancers	NH-A	brain
50	chr2:100906800-100907800	Enhancers	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links