Variant report

Variant	rs4985360
Chromosome Location	chr16:74783398-74783399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:74780351..74785848-chr16:74807254..74810760,5	MCF-7	breast:
2	chr16:74781928..74783966-chr16:74797514..74800300,2	MCF-7	breast:
3	chr16:74774896..74778280-chr16:74780880..74783972,4	MCF-7	breast:
4	chr16:74782582..74784440-chr16:74799346..74801716,2	K562	blood:
5	chr16:74781857..74784482-chr16:74790014..74791956,2	K562	blood:

Variant related genes	Relation type
ENSG00000103089	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12444462	0.85[MEX][hapmap]
rs12928993	0.85[ASN][1000 genomes]
rs12930223	0.85[ASN][1000 genomes]
rs13330685	0.90[ASN][1000 genomes]
rs13330763	0.84[ASN][1000 genomes]
rs35546013	0.90[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	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1061948	chr16:74660609-74882915	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
5	nsv542957	chr16:74660609-74882915	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
6	nsv906906	chr16:74664743-74805668	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
7	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv906907	chr16:74702254-74785902	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
9	nsv517513	chr16:74743736-74812676	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
10	nsv1058900	chr16:74753819-75005050	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
11	nsv542958	chr16:74753819-75005050	Weak transcription Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	esv3345041	chr16:74756263-75066969	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
13	nsv457520	chr16:74758984-74907440	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
14	nsv572976	chr16:74758984-74907440	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4985360	LDHD	cis	cerebellum	SCAN
rs4985360	MON1B	cis	cerebellum	SCAN
rs4985360	HPR	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74772400-74783400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr16:74775200-74784800	Enhancers	Brain Substantia Nigra	brain
3	chr16:74776200-74783600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr16:74777600-74802400	Weak transcription	Thymus	Thymus
5	chr16:74778000-74783400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr16:74778000-74783600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr16:74778400-74783400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr16:74778600-74784800	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr16:74779600-74783400	Weak transcription	Gastric	stomach
10	chr16:74779600-74783800	Weak transcription	NHLF	lung
11	chr16:74779600-74792800	Weak transcription	Pancreas	Pancrea
12	chr16:74779600-74803800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr16:74779600-74805400	Weak transcription	Colonic Mucosa	Colon
14	chr16:74780000-74783400	Weak transcription	Fetal Intestine Large	intestine
15	chr16:74780000-74805200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr16:74780200-74787400	Weak transcription	Stomach Mucosa	stomach
17	chr16:74780200-74802400	Weak transcription	Fetal Intestine Small	intestine
18	chr16:74781400-74784200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr16:74781600-74785000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr16:74781800-74783800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr16:74781800-74784000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr16:74781800-74784200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr16:74781800-74784800	Enhancers	Fetal Thymus	thymus
24	chr16:74782000-74783400	Weak transcription	Brain Anterior Caudate	brain
25	chr16:74782000-74783400	Weak transcription	A549	lung
26	chr16:74782200-74783800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr16:74782200-74784000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr16:74782200-74784000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr16:74782400-74784000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr16:74782600-74783400	Enhancers	Brain Hippocampus Middle	brain
31	chr16:74782800-74783400	Enhancers	Esophagus	oesophagus
32	chr16:74782800-74783600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr16:74782800-74783600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr16:74782800-74783600	Enhancers	HMEC	breast
35	chr16:74782800-74784600	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr16:74782800-74784800	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr16:74782800-74789600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr16:74783000-74783600	Enhancers	NHEK	skin
39	chr16:74783000-74783800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr16:74783000-74784000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr16:74783000-74784000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr16:74783000-74784000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr16:74783000-74784200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr16:74783000-74784600	Bivalent Enhancer	HepG2	liver
45	chr16:74783000-74784800	Enhancers	Brain Cingulate Gyrus	brain
46	chr16:74783200-74783400	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr16:74783200-74784200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr16:74783200-74784200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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