Variant report

Variant	rs2341768
Chromosome Location	chr6:149810195-149810196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr6:149809796-149810436	MCF-7	breast:	n/a	chr6:149810021-149810029 chr6:149810032-149810043
2	PAX5	chr6:149809992-149810306	GM12878	blood:	n/a	n/a
3	GATA3	chr6:149809830-149810204	T-47D	breast:	n/a	chr6:149810021-149810029 chr6:149810032-149810043

Variant related genes	Relation type
ZC3H12D	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10485097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10782310	0.81[CHB][hapmap]
rs10782312	0.81[CHB][hapmap]
rs11155662	0.81[CHB][hapmap]
rs11155670	0.81[CHB][hapmap]
rs11155671	0.81[CHB][hapmap]
rs1125107	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12234128	0.81[CHB][hapmap]
rs12524946	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12529698	0.81[CHB][hapmap]
rs12663698	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12665533	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1474640	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17732745	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2064520	0.81[CHB][hapmap]
rs2105200	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2179368	0.81[CEU][hapmap]
rs2341550	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2341551	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28580659	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2880075	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34870994	0.83[ASN][1000 genomes]
rs3734295	0.81[CHB][hapmap]
rs3777949	0.81[CHB][hapmap]
rs3798761	0.81[CHB][hapmap]
rs3813675	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3924871	0.81[CHB][hapmap]
rs4869797	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4897128	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4897130	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4897131	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4897132	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4897133	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4897137	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4897138	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4897139	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60404985	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62439778	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62442787	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62442788	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62442789	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62442790	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62442792	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62442793	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62442795	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62442798	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6570968	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6911016	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6929614	0.96[ASN][1000 genomes]
rs761617	0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7740278	0.81[CHB][hapmap]
rs7753560	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7767622	0.81[CHB][hapmap]
rs7774559	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7774597	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs909792	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9285521	0.81[CHB][hapmap]
rs9322184	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9322185	0.93[ASN][1000 genomes]
rs9322188	0.80[CHB][hapmap]
rs9322198	0.81[CHB][hapmap]
rs9322200	0.80[CHB][hapmap]
rs9373594	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9373595	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9373596	0.88[ASN][1000 genomes]
rs9377220	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9377221	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9377223	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9377224	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9377230	0.81[CHB][hapmap]
rs9390684	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9390687	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390688	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9390689	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9393175	0.80[CHB][hapmap]
rs9399689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9399690	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9404042	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9404043	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9404044	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9404048	0.81[CHB][hapmap]
rs9406344	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9498368	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9689569	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9689723	0.81[CHB][hapmap]
rs9718079	0.81[CHB][hapmap]
rs9767105	0.81[CHB][hapmap]
rs9767123	0.81[CHB][hapmap]
rs9767555	0.81[CHB][hapmap]
rs9767713	0.81[CHB][hapmap]
rs9800580	0.81[CHB][hapmap]
rs9800614	0.81[CHB][hapmap]
rs9800648	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9800686	0.81[CHB][hapmap]
rs9800736	0.81[CHB][hapmap]
rs9968911	0.81[CHB][hapmap]

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	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv1832313	chr6:149789511-149840750	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2341768	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149804400-149824600	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:149806400-149832000	Weak transcription	HSMMtube	muscle
3	chr6:149806400-149844800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:149806800-149825200	Weak transcription	HSMM	muscle
5	chr6:149806800-149832400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:149807000-149811200	Weak transcription	Right Atrium	heart
7	chr6:149807000-149812200	Enhancers	Primary B cells from peripheral blood	blood
8	chr6:149807000-149814000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:149807000-149814600	Weak transcription	Fetal Thymus	thymus
10	chr6:149807000-149832200	Weak transcription	Lung	lung
11	chr6:149807000-149849000	Weak transcription	Gastric	stomach
12	chr6:149807200-149810200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:149807200-149811200	Enhancers	GM12878-XiMat	blood
14	chr6:149807200-149811600	Enhancers	Primary B cells from cord blood	blood
15	chr6:149807200-149815600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:149807200-149824800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr6:149807200-149832000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:149807200-149835000	Weak transcription	Spleen	Spleen
19	chr6:149807200-149842600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:149807600-149813800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:149808000-149814000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:149809600-149811200	Enhancers	Fetal Intestine Large	intestine
23	chr6:149809600-149811200	Enhancers	HepG2	liver
24	chr6:149809600-149811400	Enhancers	Fetal Intestine Small	intestine
25	chr6:149809800-149810200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:149809800-149810200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:149809800-149810200	Enhancers	Fetal Muscle Trunk	muscle
28	chr6:149809800-149810200	Enhancers	Stomach Mucosa	stomach
29	chr6:149809800-149810400	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr6:149809800-149810600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:149809800-149810800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr6:149809800-149810800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:149809800-149810800	Enhancers	Esophagus	oesophagus
34	chr6:149809800-149811200	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr6:149809800-149811400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:149810000-149810400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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