Variant report

Variant	rs72941454
Chromosome Location	chr3:100081811-100081812
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100075933..100077541-chr3:100081151..100083943,3	K562	blood:
2	chr3:100080264..100084111-chr3:100088044..100091810,5	MCF-7	breast:
3	chr3:100079303..100082344-chr3:100118989..100121864,3	K562	blood:
4	chr3:100076004..100077691-chr3:100081043..100083943,2	K562	blood:
5	chr3:100080257..100082671-chr3:100085053..100087011,2	K562	blood:
6	chr3:100053013..100055623-chr3:100080603..100084402,3	K562	blood:

Variant related genes	Relation type
ENSG00000154174	Chromatin interaction
ENSG00000114021	Chromatin interaction
ENSG00000206535	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11918399	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11919543	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11919627	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16842142	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3772687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55699261	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55864663	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56012915	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56956506	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57155242	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57166766	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57332305	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57703319	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59304656	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59396265	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59491720	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59507591	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59509062	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60463428	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60999188	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72941434	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72941452	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72941453	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72941473	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72941482	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9873033	0.83[ASN][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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:100054800-100097200	Weak transcription	Stomach Mucosa	stomach
3	chr3:100054800-100102200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:100055000-100082400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:100069400-100082400	Weak transcription	Fetal Brain Male	brain
6	chr3:100069600-100083800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:100069600-100085800	Weak transcription	Small Intestine	intestine
8	chr3:100069600-100087000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:100071000-100087800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:100071000-100087800	Strong transcription	Fetal Muscle Trunk	muscle
11	chr3:100071000-100093600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:100071000-100103200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:100071000-100104400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:100071400-100082200	Strong transcription	NHEK	skin
15	chr3:100071400-100088000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:100071400-100105800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:100071600-100087000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:100071800-100084200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:100071800-100090600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:100072000-100084200	Weak transcription	K562	blood
21	chr3:100072600-100084800	Weak transcription	Hela-S3	cervix
22	chr3:100073200-100082400	Weak transcription	NHLF	lung
23	chr3:100073200-100090200	Weak transcription	Esophagus	oesophagus
24	chr3:100073400-100090400	Weak transcription	Pancreas	Pancrea
25	chr3:100073400-100096400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:100073800-100090600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:100073800-100098200	Weak transcription	Gastric	stomach
28	chr3:100074000-100083200	Weak transcription	Colonic Mucosa	Colon
29	chr3:100074000-100084000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:100074400-100083800	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:100074600-100082800	Weak transcription	Psoas Muscle	Psoas
32	chr3:100074600-100084200	Weak transcription	Spleen	Spleen
33	chr3:100074800-100083200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:100075200-100084200	Weak transcription	Right Ventricle	heart
35	chr3:100075400-100082400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:100075400-100084200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:100075400-100086200	Weak transcription	Brain Substantia Nigra	brain
38	chr3:100077000-100106000	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr3:100077200-100088000	Strong transcription	Primary B cells from cord blood	blood
40	chr3:100077200-100105600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr3:100077400-100087200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr3:100077600-100105200	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:100078000-100082000	Strong transcription	HMEC	breast
44	chr3:100078400-100084200	Weak transcription	HepG2	liver
45	chr3:100078400-100089600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:100078600-100087600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr3:100078800-100082000	Strong transcription	Brain Germinal Matrix	brain
48	chr3:100078800-100087800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:100078800-100103000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:100078800-100104400	Strong transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links