Variant report

Variant	rs16897919
Chromosome Location	chr6:30788588-30788589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30687583..30690453-chr6:30788279..30790519,3	MCF-7	breast:
2	chr6:30788219..30790360-chr6:31110500..31112207,2	MCF-7	breast:
3	chr6:30786994..30789878-chr6:30922347..30924332,2	K562	blood:
4	chr6:30715944..30717540-chr6:30787940..30790254,2	K562	blood:
5	chr6:30690499..30693062-chr6:30788565..30790679,2	MCF-7	breast:
6	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
7	chr6:30782149..30783848-chr6:30788583..30790085,2	MCF-7	breast:
8	chr6:30784917..30788265-chr6:30788350..30790459,3	K562	blood:
9	chr6:30735402..30739247-chr6:30785239..30791444,10	MCF-7	breast:
10	chr6:30785152..30790346-chr6:30842867..30847278,6	K562	blood:
11	chr6:30788098..30790149-chr6:30839123..30842076,2	K562	blood:
12	chr6:30780598..30803497-chr6:30842531..30855110,80	MCF-7	breast:
13	chr6:30710229..30713248-chr6:30788195..30791151,4	K562	blood:
14	chr6:30787837..30792214-chr6:30792255..30797817,7	K562	blood:
15	chr6:30747572..30751987-chr6:30785552..30789586,6	MCF-7	breast:
16	chr6:30709253..30713765-chr6:30784905..30790853,10	K562	blood:
17	chr6:30775890..30781762-chr6:30785090..30789723,9	MCF-7	breast:
18	chr6:30762133..30768787-chr6:30785989..30790050,8	MCF-7	breast:
19	chr6:30703055..30723531-chr6:30783853..30800217,151	MCF-7	breast:
20	chr6:30784327..30791562-chr6:30848580..30853873,26	MCF-7	breast:
21	chr6:30787789..30791714-chr6:30792255..30797305,10	K562	blood:
22	chr6:30698701..30700492-chr6:30786748..30789246,2	MCF-7	breast:
23	chr6:30779954..30784896-chr6:30785156..30789787,6	K562	blood:
24	chr6:30735347..30739906-chr6:30783605..30789456,10	MCF-7	breast:
25	chr6:30786635..30788882-chr6:31053908..31056408,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272273	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000228022	Chromatin interaction
ENSG00000233529	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000201988	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000272540	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000263608	Chromatin interaction
ENSG00000237775	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13212094	1.00[AFR][1000 genomes]
rs16897933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711238	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711239	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711248	1.00[AFR][1000 genomes]
rs4711250	1.00[AFR][1000 genomes]
rs4713374	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713375	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713377	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57662504	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61177273	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295937	1.00[AFR][1000 genomes]
rs9348844	1.00[AFR][1000 genomes]
rs9357103	1.00[AFR][1000 genomes]
rs9366762	1.00[AFR][1000 genomes]
rs9368645	1.00[AFR][1000 genomes]
rs9368648	1.00[AFR][1000 genomes]
rs9378150	1.00[AFR][1000 genomes]
rs9391637	1.00[AFR][1000 genomes]
rs9394024	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS 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	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	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
8	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
9	esv2757160	chr6:30785273-30788588	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
10	nsv10812	chr6:30785661-30789859	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16897919	GTF2H4	cis	multi-tissue	Pritchard

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30779000-30794800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:30779000-30795800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:30779200-30790000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:30782000-30796000	Weak transcription	Pancreas	Pancrea
5	chr6:30782000-30797000	Weak transcription	Gastric	stomach
6	chr6:30782200-30789600	Weak transcription	Brain Substantia Nigra	brain
7	chr6:30782400-30790000	Weak transcription	Primary T cells from cord blood	blood
8	chr6:30782600-30789400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:30782600-30789600	Weak transcription	Fetal Intestine Large	intestine
10	chr6:30782600-30789800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:30782800-30794600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:30783200-30789600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:30783200-30789800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr6:30783400-30794600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:30784800-30788800	Enhancers	Placenta	Placenta
16	chr6:30785000-30788800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr6:30785200-30788600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:30785200-30789600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:30785400-30788600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:30785400-30789600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr6:30785400-30789800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:30785400-30790800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:30785600-30788600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr6:30785600-30790000	Enhancers	HMEC	breast
25	chr6:30785800-30789200	Weak transcription	GM12878-XiMat	blood
26	chr6:30786000-30788600	Enhancers	NH-A	brain
27	chr6:30786200-30788800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr6:30786200-30788800	Enhancers	A549	lung
29	chr6:30786200-30788800	Enhancers	HUVEC	blood vessel
30	chr6:30786200-30789000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:30786200-30789000	Enhancers	Osteobl	bone
32	chr6:30786200-30790000	Enhancers	K562	blood
33	chr6:30786200-30790800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:30786400-30788600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:30786400-30788600	Enhancers	Fetal Heart	heart
36	chr6:30786400-30788600	Enhancers	NHDF-Ad	bronchial
37	chr6:30786400-30788600	Enhancers	NHLF	lung
38	chr6:30786400-30790800	Enhancers	HSMMtube	muscle
39	chr6:30786400-30791400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:30786400-30792800	Enhancers	Stomach Mucosa	stomach
41	chr6:30786600-30788800	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr6:30786600-30789400	Weak transcription	Aorta	Aorta
43	chr6:30786600-30789800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:30786800-30789600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr6:30786800-30789600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr6:30786800-30789600	Weak transcription	Fetal Kidney	kidney
47	chr6:30786800-30789600	Weak transcription	Fetal Lung	lung
48	chr6:30787000-30788600	Enhancers	HSMM	muscle
49	chr6:30787000-30789600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:30787000-30789600	Weak transcription	Rectal Smooth Muscle	rectum

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