Variant report

Variant	rs3845860
Chromosome Location	chr3:121229806-121229807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121228286..121231093-chr3:121234825..121237774,2	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10451895	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10934551	0.95[ASN][1000 genomes]
rs11705939	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11706583	0.91[ASN][1000 genomes]
rs11709378	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11711667	0.98[ASN][1000 genomes]
rs11713643	0.88[ASN][1000 genomes]
rs11714746	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11714774	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11715085	0.84[EUR][1000 genomes]
rs11718918	0.98[ASN][1000 genomes]
rs12488196	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12496163	0.95[ASN][1000 genomes]
rs12632308	0.98[ASN][1000 genomes]
rs12634017	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12635218	0.98[ASN][1000 genomes]
rs13059229	0.91[ASN][1000 genomes]
rs13077237	0.85[ASN][1000 genomes]
rs13077305	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13080007	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs13082118	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13085365	0.91[ASN][1000 genomes]
rs13095550	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13097659	0.98[ASN][1000 genomes]
rs13100579	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1381057	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1381058	0.88[ASN][1000 genomes]
rs1381059	0.98[ASN][1000 genomes]
rs1877968	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1877969	0.86[ASN][1000 genomes]
rs2169301	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2331962	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs28406368	0.98[ASN][1000 genomes]
rs3218649	0.98[ASN][1000 genomes]
rs35362700	0.83[ASN][1000 genomes]
rs3732405	0.81[ASN][1000 genomes]
rs3732406	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3772122	0.98[ASN][1000 genomes]
rs3772124	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806614	0.89[ASN][1000 genomes]
rs3843345	0.88[ASN][1000 genomes]
rs3845863	0.86[ASN][1000 genomes]
rs3911713	0.98[ASN][1000 genomes]
rs4555467	0.98[ASN][1000 genomes]
rs4676677	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4676680	0.80[ASN][1000 genomes]
rs4676722	0.86[ASN][1000 genomes]
rs4676728	0.86[ASN][1000 genomes]
rs488636	0.93[ASN][1000 genomes]
rs500100	0.83[ASN][1000 genomes]
rs500103	0.83[ASN][1000 genomes]
rs502643	0.93[ASN][1000 genomes]
rs524026	0.93[ASN][1000 genomes]
rs541818	0.89[ASN][1000 genomes]
rs575913	1.00[ASN][1000 genomes]
rs587553	0.91[ASN][1000 genomes]
rs61796946	0.95[ASN][1000 genomes]
rs6438630	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6438633	0.88[ASN][1000 genomes]
rs66922316	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778684	0.98[ASN][1000 genomes]
rs6784324	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6793252	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797376	0.88[ASN][1000 genomes]
rs6797682	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs693403	1.00[ASN][1000 genomes]
rs702019	0.93[ASN][1000 genomes]
rs7612018	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7613752	0.88[ASN][1000 genomes]
rs7614639	0.83[ASN][1000 genomes]
rs7615529	0.95[ASN][1000 genomes]
rs7617748	0.91[ASN][1000 genomes]
rs7622867	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7622881	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7622897	0.98[ASN][1000 genomes]
rs7628081	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7633930	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7645027	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7645050	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7645869	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998555	chr3:120700604-121348015	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv591400	chr3:121070299-121339354	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv877381	chr3:121192350-121343500	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1007522	chr3:121200563-121374051	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121151200-121263800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:121177200-121237000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:121178200-121263800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:121183800-121234400	Weak transcription	Primary B cells from cord blood	blood
5	chr3:121186400-121255600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:121192200-121233600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:121193200-121237000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:121195600-121233800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:121197200-121233400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:121200600-121264000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:121201000-121250600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:121202400-121263200	Weak transcription	NHLF	lung
13	chr3:121202400-121263800	Weak transcription	HSMM	muscle
14	chr3:121202600-121233400	Weak transcription	NHEK	skin
15	chr3:121202800-121236600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:121207200-121233400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:121208600-121233400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:121209400-121263600	Weak transcription	NHDF-Ad	bronchial
19	chr3:121209800-121233400	Weak transcription	Thymus	Thymus
20	chr3:121210000-121246400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:121210200-121241400	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:121214000-121230400	Weak transcription	Fetal Stomach	stomach
23	chr3:121220800-121230800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:121221000-121232200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:121221400-121233400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:121222200-121232200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:121222400-121231400	Weak transcription	Hela-S3	cervix
28	chr3:121223400-121231400	Strong transcription	GM12878-XiMat	blood
29	chr3:121223800-121231600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:121224600-121234000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:121225200-121234800	Weak transcription	Brain Germinal Matrix	brain
32	chr3:121225400-121231400	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:121225600-121236400	Weak transcription	Fetal Lung	lung
34	chr3:121225800-121236200	Weak transcription	K562	blood
35	chr3:121226600-121231400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:121227000-121231000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:121227200-121233800	Weak transcription	Fetal Intestine Large	intestine
38	chr3:121227400-121234600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:121227600-121233400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr3:121227800-121233400	Weak transcription	A549	lung
41	chr3:121229000-121230000	Weak transcription	Fetal Kidney	kidney
42	chr3:121229000-121230200	Weak transcription	Fetal Intestine Small	intestine
43	chr3:121229000-121231200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:121229000-121234600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:121229000-121238600	Weak transcription	HMEC	breast
46	chr3:121229000-121239200	Weak transcription	HUVEC	blood vessel
47	chr3:121229000-121244600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr3:121229000-121253200	Weak transcription	HepG2	liver
49	chr3:121229200-121230000	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr3:121229200-121230800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links