Variant report

Variant	rs6930977
Chromosome Location	chr6:30435288-30435289
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	ZNF263	chr6:30435081-30435395	HEK293-T-REx	kidney:	n/a	chr6:30435186-30435207

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30433130..30435301-chr6:30582917..30586018,4	MCF-7	breast:
2	chr6:30431634..30435485-chr6:30582972..30586314,3	K562	blood:

Variant related genes	Relation type
SUCLA2P1	TF binding region
ENSG00000222894	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000204568	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1076832	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12210448	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12214298	0.88[AMR][1000 genomes]
rs12214645	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17188743	0.80[AMR][1000 genomes]
rs17195068	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17195089	0.80[AMR][1000 genomes]
rs17410877	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2157605	0.85[AMR][1000 genomes]
rs34039931	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34111681	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34124993	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34521355	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35118048	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35764894	0.80[EUR][1000 genomes]
rs4711217	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6941668	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' 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	1030 gene(s)	inside rSNPs	diseases
4	nsv601478	chr6:30383768-30438226	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
6	nsv884065	chr6:30430520-30446055	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv884066	chr6:30430875-30440732	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv884067	chr6:30430875-30446055	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv884068	chr6:30430875-30447987	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv884069	chr6:30430875-30451474	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
11	nsv884070	chr6:30430875-30472772	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
12	nsv884071	chr6:30433090-30444357	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
13	nsv884072	chr6:30433611-30447987	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
14	nsv884073	chr6:30434566-30445476	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv884074	chr6:30434566-30447987	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
16	nsv884075	chr6:30434566-30449046	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
17	nsv884076	chr6:30434566-30483919	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
18	nsv884077	chr6:30434900-30512163	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
19	nsv884078	chr6:30435288-30446055	Bivalent Enhancer Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	nsv884079	chr6:30435288-30447987	Bivalent Enhancer Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6930977	HLA-H	cis	multi-tissue	Pritchard
rs6930977	HLA-E	cis	multi-tissue	Pritchard
rs6930977	HLA-DRB5	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30434600-30435400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:30434800-30435400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:30434800-30435400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
4	chr6:30434800-30435400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:30434800-30435400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
6	chr6:30434800-30435400	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
7	chr6:30434800-30435600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr6:30434800-30435600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
9	chr6:30434800-30435600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:30434800-30435600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:30434800-30435600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:30434800-30435600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:30435000-30435400	Bivalent Enhancer	Primary T cells from cord blood	blood
14	chr6:30435000-30435400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
15	chr6:30435000-30435400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
16	chr6:30435200-30435400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
17	chr6:30435200-30435400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
18	chr6:30435200-30435400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
19	chr6:30435200-30435400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
20	chr6:30435200-30435600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:30435200-30435600	Bivalent Enhancer	Colonic Mucosa	Colon
22	chr6:30435200-30436000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links