Variant report

Variant	rs1978486
Chromosome Location	chr16:31130910-31130911
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:31127491..31131830-chr16:31190393..31192870,6	MCF-7	breast:
2	chr16:31127220..31133615-chr16:31189948..31195209,18	K562	blood:
3	chr16:31104440..31108567-chr16:31128079..31131886,5	MCF-7	breast:
4	chr16:30816280..30819245-chr16:31129948..31132814,2	K562	blood:
5	chr16:30966438..30967999-chr16:31130219..31132345,2	K562	blood:
6	chr16:31129797..31131930-chr17:56707897..56709423,2	MCF-7	breast:
7	chr16:30968063..30971621-chr16:31128915..31132343,4	K562	blood:

Variant related genes	Relation type
ENSG00000089280	Chromatin interaction
ENSG00000099381	Chromatin interaction
ENSG00000260304	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000255439	Chromatin interaction
ENSG00000167397	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1549295	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs1549296	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4889540	0.85[YRI][hapmap]
rs4889621	1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4889632	0.85[YRI][hapmap]
rs8044643	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
4	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
5	nsv905734	chr16:30877544-31191482	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
6	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer 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 miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
7	nsv457483	chr16:30903679-31191482	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
8	nsv571820	chr16:30903679-31191482	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription 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	253 gene(s)	inside rSNPs	diseases
9	esv1797877	chr16:30948643-31188432	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
10	nsv833193	chr16:30960796-31133604	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
11	nsv905740	chr16:31066249-31232437	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
12	nsv905741	chr16:31066249-31247924	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription 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 target site	202 gene(s)	inside rSNPs	diseases
13	nsv905742	chr16:31102321-31247924	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	188 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1978486	TRIM72	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31129800-31131200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr16:31129800-31131400	Weak transcription	Esophagus	oesophagus
3	chr16:31129800-31131400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr16:31130000-31131000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr16:31130000-31131000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
6	chr16:31130000-31131000	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr16:31130000-31131400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:31130000-31131400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr16:31130000-31131400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr16:31130000-31131400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr16:31130000-31131400	Weak transcription	Aorta	Aorta
12	chr16:31130000-31131800	Genic enhancers	Pancreas	Pancrea
13	chr16:31130000-31132800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr16:31130200-31131000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr16:31130200-31131000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr16:31130200-31131000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr16:31130200-31131000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr16:31130200-31131200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr16:31130200-31131200	Genic enhancers	Primary monocytes fromperipheralblood	blood
20	chr16:31130200-31131200	Enhancers	Psoas Muscle	Psoas
21	chr16:31130200-31131400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr16:31130200-31131400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr16:31130200-31131400	Weak transcription	HUVEC	blood vessel
24	chr16:31130200-31133800	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr16:31130200-31133800	Strong transcription	Brain Germinal Matrix	brain
26	chr16:31130200-31134000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr16:31130200-31135600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr16:31130200-31136600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr16:31130400-31131000	Enhancers	Primary B cells from cord blood	blood
30	chr16:31130400-31131000	Genic enhancers	NHEK	skin
31	chr16:31130400-31131200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr16:31130400-31131200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr16:31130400-31131200	Weak transcription	Gastric	stomach
34	chr16:31130400-31131200	Weak transcription	Spleen	Spleen
35	chr16:31130400-31131200	Weak transcription	HepG2	liver
36	chr16:31130400-31131400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr16:31130400-31131400	Weak transcription	Brain Angular Gyrus	brain
38	chr16:31130400-31131400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr16:31130400-31131400	Weak transcription	Brain Substantia Nigra	brain
40	chr16:31130400-31131400	Weak transcription	Colon Smooth Muscle	Colon
41	chr16:31130400-31131400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr16:31130400-31131400	Weak transcription	Fetal Brain Male	brain
43	chr16:31130400-31131400	Weak transcription	Fetal Kidney	kidney
44	chr16:31130400-31131400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr16:31130400-31131400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr16:31130400-31131400	Weak transcription	Right Ventricle	heart
47	chr16:31130400-31131400	Weak transcription	Small Intestine	intestine
48	chr16:31130400-31131400	Weak transcription	A549	lung
49	chr16:31130400-31131400	Weak transcription	GM12878-XiMat	blood
50	chr16:31130400-31131400	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links