Variant report

Variant	rs60149397
Chromosome Location	chr6:31678960-31678961
allele	A/G
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	GATA2	chr6:31678940-31679262	HUVEC	blood vessel:	n/a	n/a
2	GATA1	chr6:31678697-31679610	PBDE	blood:	n/a	n/a
3	SPI1	chr6:31678909-31679412	HL-60	blood:	n/a	chr6:31678995-31679008
4	ELF1	chr6:31678899-31679320	K562	blood:	n/a	n/a
5	MAX	chr6:31678901-31679284	K562	blood:	n/a	n/a
6	BHLHE40	chr6:31678889-31679193	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:31676949..31679536-chr6:31784835..31786344,2	MCF-7	breast:
2	chr6:31632238..31634263-chr6:31678523..31680253,2	MCF-7	breast:
3	chr6:31677895..31680160-chr6:31702614..31704121,2	MCF-7	breast:
4	chr6:31669599..31672574-chr6:31678491..31681695,4	MCF-7	breast:

Variant related genes	Relation type
LY6G6D	TF binding region
ENSG00000263020	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000204427	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11964779	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11965323	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966331	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11967206	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2254083	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295666	1.00[ASN][1000 genomes]
rs2295667	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28399971	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34453162	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3895064	0.83[ASN][1000 genomes]
rs4713482	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4713492	0.83[ASN][1000 genomes]
rs4947252	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4947329	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947330	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59002496	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59114240	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60559550	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60900316	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73398259	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7382084	1.00[EUR][1000 genomes]
rs9800604	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
12	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
13	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
14	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31671600-31681600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:31671800-31695800	Weak transcription	Right Atrium	heart
3	chr6:31672000-31679000	Weak transcription	Esophagus	oesophagus
4	chr6:31672000-31682800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:31672000-31685400	Weak transcription	Gastric	stomach
6	chr6:31677600-31679000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:31677600-31679000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:31677600-31682400	Enhancers	K562	blood
9	chr6:31677600-31683600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr6:31677800-31679400	Enhancers	Lung	lung
11	chr6:31677800-31680000	Enhancers	Primary hematopoietic stem cells	blood
12	chr6:31677800-31680200	Enhancers	Spleen	Spleen
13	chr6:31677800-31680600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:31678000-31679000	Enhancers	NHEK	skin
15	chr6:31678200-31679000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
16	chr6:31678200-31679400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:31678200-31679600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
18	chr6:31678200-31679600	Enhancers	Fetal Thymus	thymus
19	chr6:31678200-31680200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr6:31678200-31680200	Enhancers	Primary B cells from peripheral blood	blood
21	chr6:31678400-31679200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:31678400-31679200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr6:31678400-31679400	Enhancers	Colonic Mucosa	Colon
24	chr6:31678400-31679400	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr6:31678400-31679600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr6:31678400-31679800	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr6:31678400-31680200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:31678400-31680400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:31678400-31683200	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr6:31678400-31684200	Enhancers	Fetal Brain Male	brain
31	chr6:31678600-31679000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:31678600-31679000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:31678600-31679200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:31678600-31679200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:31678600-31679200	Enhancers	Fetal Intestine Large	intestine
36	chr6:31678600-31679200	Enhancers	Fetal Intestine Small	intestine
37	chr6:31678600-31679400	Enhancers	Primary B cells from cord blood	blood
38	chr6:31678600-31679400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr6:31678600-31679400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:31678600-31679400	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr6:31678600-31679400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
42	chr6:31678600-31679400	Flanking Active TSS	Fetal Brain Female	brain
43	chr6:31678600-31679600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:31678600-31679600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr6:31678600-31679600	Enhancers	HUVEC	blood vessel
46	chr6:31678600-31679600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr6:31678600-31679800	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr6:31678600-31680200	Enhancers	Placenta	Placenta
49	chr6:31678600-31680200	Enhancers	Stomach Mucosa	stomach
50	chr6:31678800-31679000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle

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