Variant report

Variant	rs6587630
Chromosome Location	chr1:151883273-151883274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151881809-151883419	K562	blood:	n/a	n/a
2	HCFC1	chr1:151881417-151883304	Hela-S3	cervix:	n/a	n/a
3	WRNIP1	chr1:151883270-151883280	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151861522..151872673-chr1:151876647..151885029,20	MCF-7	breast:
2	chr1:151882662..151885279-chr19:12903227..12904893,2	MCF-7	breast:
3	chr1:151881661..151883557-chr1:152019981..152021490,2	K562	blood:
4	chr1:151863646..151865677-chr1:151881470..151883641,2	K562	blood:
5	chr1:151879131..151885542-chr1:151961269..151968730,13	MCF-7	breast:
6	chr1:151877897..151883557-chr1:152019456..152022411,7	K562	blood:
7	chr1:151880209..151887387-chr1:151961986..151968084,15	MCF-7	breast:
8	chr1:151879353..151883785-chr1:152005989..152009719,8	K562	blood:
9	chr1:151879656..151883388-chr1:152007614..152010954,7	K562	blood:
10	chr1:151810931..151813859-chr1:151881520..151883452,3	MCF-7	breast:
11	chr1:151882722..151885720-chr1:151898176..151900104,2	MCF-7	breast:

No data

Variant related genes	Relation type
THEM4	TF binding region
ENSG00000197747	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000229021	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000095066	Chromatin interaction
ENSG00000225556	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1003107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10158030	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1038746	1.00[CHB][hapmap]
rs1038748	1.00[CHB][hapmap]
rs1048910	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10749666	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10788813	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs10788814	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10788816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10888448	0.85[AMR][1000 genomes]
rs10888449	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10888450	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10888451	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10888453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11204905	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs11204911	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204912	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204923	1.00[CHB][hapmap]
rs12723616	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs1352654	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1387834	1.00[CHB][hapmap]
rs1387835	1.00[CHB][hapmap]
rs1490187	1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs1490190	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1490191	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1496037	1.00[CHB][hapmap]
rs1552606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1552607	1.00[CHB][hapmap]
rs1602245	1.00[CHB][hapmap]
rs1602248	1.00[CHB][hapmap]
rs17583707	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1844542	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1873310	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1873311	1.00[CHB][hapmap]
rs1873312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1967085	1.00[CHB][hapmap]
rs2054948	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2087549	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2087550	0.82[ASN][1000 genomes]
rs2130526	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2171917	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2338018	1.00[CHB][hapmap]
rs2338200	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2338203	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2338204	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2338210	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932563	1.00[CHB][hapmap]
rs2932567	1.00[CHB][hapmap]
rs2932578	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2932584	0.91[ASN][1000 genomes]
rs2932592	1.00[CHB][hapmap]
rs2999509	0.82[ASN][1000 genomes]
rs2999514	1.00[CHB][hapmap]
rs2999527	1.00[CHB][hapmap]
rs2999529	1.00[CHB][hapmap]
rs2999535	1.00[CHB][hapmap]
rs2999536	1.00[CHB][hapmap]
rs2999537	1.00[CHB][hapmap]
rs2999538	1.00[CHB][hapmap]
rs2999551	1.00[CHB][hapmap]
rs2999552	1.00[CHB][hapmap]
rs2999555	1.00[CHB][hapmap]
rs2999558	1.00[CHB][hapmap]
rs3001979	1.00[CHB][hapmap]
rs3007672	1.00[CHB][hapmap]
rs3007676	1.00[CHB][hapmap]
rs3007679	1.00[CHB][hapmap]
rs3007682	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007690	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3007692	0.91[ASN][1000 genomes]
rs3007700	1.00[CHB][hapmap]
rs3007701	1.00[CHB][hapmap]
rs3007704	1.00[CHB][hapmap]
rs3122300	1.00[CHB][hapmap]
rs3122301	1.00[CHB][hapmap]
rs34370890	0.94[ASN][1000 genomes]
rs3748805	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3762427	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4551598	0.86[EUR][1000 genomes]
rs4845385	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4845388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4845393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4845660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845664	1.00[CHB][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845699	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587626	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6587627	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6587628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587641	1.00[CHB][hapmap]
rs6659029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6662463	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6678664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6690443	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6691350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7529451	1.00[CHB][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7532721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7541498	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7544380	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7545863	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7552869	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs902314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs902315	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs902316	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs959945	1.00[CHB][hapmap]
rs9943225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers 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	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6587630	THEM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151880600-151883400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:151881000-151883400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:151882600-151883400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr1:151882800-151883400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:151882800-151883800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:151883000-151883400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:151883000-151883400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:151883000-151883400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:151883000-151883600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr1:151883000-151883600	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr1:151883000-151883800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:151883200-151883400	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr1:151883200-151883600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr1:151883200-151883600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr1:151883200-151883600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr1:151883200-151883600	Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr1:151883200-151883600	Enhancers	K562	blood
18	chr1:151883200-151887200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:151883200-151887800	Weak transcription	Aorta	Aorta
20	chr1:151883200-151892200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links