Variant report

Variant	rs6929434
Chromosome Location	chr6:31127947-31127948
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr6:31127782-31128079	GM12878	blood:	n/a	n/a
2	CTCF	chr6:31127860-31128010	HEEpiC	esophagus:	n/a	n/a
3	MTA3	chr6:31126058-31128087	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:31125655-31128143	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:31126717-31127953	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:31126119-31128136	GM12892	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31125954..31128399-chr6:31147370..31149956,2	MCF-7	breast:
2	chr6:31127915..31129464-chr6:31137096..31138939,2	K562	blood:
3	chr6:31126958..31132315-chr6:31135299..31140140,6	K562	blood:
4	chr6:31103022..31109591-chr6:31125707..31129394,9	MCF-7	breast:

No data

Variant related genes	Relation type
TCF19	TF binding region
CCHCR1	TF binding region
ENSG00000204531	Chromatin interaction
ENSG00000238211	Chromatin interaction
ENSG00000204538	Chromatin interaction
ENSG00000204540	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10456394	0.82[ASN][1000 genomes]
rs130069	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16898861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16898870	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16898922	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17190638	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17191019	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17191033	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17191082	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17191090	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17191195	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17197080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17197361	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17197381	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17840029	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28744256	0.82[ASN][1000 genomes]
rs28744263	0.82[ASN][1000 genomes]
rs2894184	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6904246	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921801	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929945	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6935662	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744751	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744752	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760698	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771083	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv884137	chr6:31082361-31129310	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv1019637	chr6:31104401-31354706	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
14	nsv1029569	chr6:31104401-31412740	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
15	nsv538174	chr6:31104401-31412740	Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
16	nsv524061	chr6:31107087-31133943	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv884138	chr6:31114573-31129707	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6929434	HLA-C	cis	multi-tissue	Pritchard
rs6929434	HCG27	cis	multi-tissue	Pritchard

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31125400-31128000	Active TSS	GM12878-XiMat	blood
2	chr6:31126400-31128000	Flanking Active TSS	Fetal Muscle Leg	muscle
3	chr6:31126600-31128000	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr6:31126600-31128000	Enhancers	Spleen	Spleen
5	chr6:31126600-31128200	Flanking Active TSS	HUVEC	blood vessel
6	chr6:31126800-31128000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:31126800-31128000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:31126800-31128000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:31126800-31128000	Flanking Active TSS	NHEK	skin
10	chr6:31127000-31128000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr6:31127000-31128000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:31127000-31128000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:31127000-31128200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:31127000-31128200	Transcr. at gene 5' and 3'	Dnd41	blood
15	chr6:31127000-31128200	Flanking Active TSS	HMEC	breast
16	chr6:31127200-31128000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:31127200-31131800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr6:31127200-31140600	Weak transcription	Left Ventricle	heart
19	chr6:31127200-31146800	Weak transcription	Small Intestine	intestine
20	chr6:31127400-31128000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr6:31127400-31128000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr6:31127400-31128000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:31127400-31128000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:31127400-31128000	Flanking Active TSS	NH-A	brain
25	chr6:31127400-31128000	Flanking Active TSS	NHDF-Ad	bronchial
26	chr6:31127400-31128000	Flanking Active TSS	NHLF	lung
27	chr6:31127400-31128200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr6:31127400-31128200	Flanking Active TSS	Hela-S3	cervix
29	chr6:31127400-31129200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:31127600-31128000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr6:31127600-31128000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:31127600-31128000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:31127600-31128000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr6:31127600-31128000	Enhancers	Esophagus	oesophagus
35	chr6:31127600-31128000	Active TSS	Fetal Brain Female	brain
36	chr6:31127600-31128000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:31127600-31128000	Enhancers	A549	lung
38	chr6:31127600-31128000	Transcr. at gene 5' and 3'	K562	blood
39	chr6:31127600-31129000	Weak transcription	Ovary	ovary
40	chr6:31127600-31129200	Weak transcription	Fetal Intestine Small	intestine
41	chr6:31127600-31129400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:31127600-31129400	Weak transcription	Gastric	stomach
43	chr6:31127600-31129600	Weak transcription	Fetal Brain Male	brain
44	chr6:31127600-31131800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr6:31127600-31132600	Weak transcription	Pancreas	Pancrea
46	chr6:31127600-31133000	Weak transcription	Fetal Intestine Large	intestine
47	chr6:31127600-31136600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr6:31127600-31137000	Weak transcription	Stomach Mucosa	stomach
49	chr6:31127600-31143000	Weak transcription	Right Ventricle	heart
50	chr6:31127600-31147800	Weak transcription	Primary B cells from cord blood	blood

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