Variant report

Variant	rs4889436
Chromosome Location	chr16:81935842-81935843
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:81928275..81931130-chr16:81935017..81936654,2	K562	blood:
2	chr16:81933931..81936851-chr16:81937531..81942910,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197943	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11641776	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4243220	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264387	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4305012	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4306503	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4424903	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4439757	0.85[ASN][1000 genomes]
rs4494532	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4510005	1.00[CHB][hapmap]
rs4520827	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4627340	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4888185	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889437	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889438	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564935	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573365	chr16:81804972-81975892	Strong transcription Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1065088	chr16:81878481-81953248	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4889436	ATMIN	cis	parietal	SCAN
rs4889436	MPHOSPH6	cis	cerebellum	SCAN
rs4889436	ATMIN	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81902800-81955600	Weak transcription	Fetal Kidney	kidney
2	chr16:81905800-81943000	Weak transcription	Small Intestine	intestine
3	chr16:81908200-81936800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr16:81908400-81950000	Strong transcription	GM12878-XiMat	blood
5	chr16:81908400-81950200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr16:81909400-81961800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr16:81911400-81936400	Weak transcription	Pancreas	Pancrea
8	chr16:81920400-81982000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr16:81922400-81944800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr16:81923000-81936800	Weak transcription	Placenta	Placenta
11	chr16:81924400-81938800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr16:81924400-81942400	Strong transcription	Duodenum Mucosa	Duodenum
13	chr16:81924400-81946200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr16:81924400-81961600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr16:81924400-81970000	Weak transcription	Fetal Intestine Large	intestine
16	chr16:81924800-81949200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr16:81925400-81949200	Weak transcription	Right Ventricle	heart
18	chr16:81925800-81936800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr16:81925800-81992600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr16:81926200-81942600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr16:81928000-81953200	Weak transcription	Fetal Thymus	thymus
22	chr16:81929600-81938200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr16:81930800-81953400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr16:81931000-81949800	Strong transcription	Liver	Liver
25	chr16:81933000-81983600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr16:81933600-81938600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr16:81934200-81936000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr16:81934400-81936000	Enhancers	Gastric	stomach
29	chr16:81934600-81936000	Enhancers	Fetal Stomach	stomach
30	chr16:81934600-81936000	Enhancers	Hela-S3	cervix
31	chr16:81934600-81936000	Enhancers	NHLF	lung
32	chr16:81934600-81936600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr16:81934600-81961200	Weak transcription	Colonic Mucosa	Colon
34	chr16:81934800-81938800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr16:81934800-81939400	Strong transcription	Spleen	Spleen
36	chr16:81934800-81945000	Weak transcription	Thymus	Thymus
37	chr16:81934800-81971600	Weak transcription	Right Atrium	heart
38	chr16:81935000-81936600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr16:81935000-81953000	Weak transcription	Adipose Nuclei	Adipose
40	chr16:81935200-81936800	Weak transcription	Lung	lung
41	chr16:81935200-81941800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr16:81935400-81936000	Flanking Active TSS	HUVEC	blood vessel
43	chr16:81935600-81936000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
44	chr16:81935600-81936000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
45	chr16:81935600-81936000	Enhancers	Esophagus	oesophagus
46	chr16:81935600-81936400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
47	chr16:81935600-81936800	ZNF genes & repeats	Primary B cells from cord blood	blood
48	chr16:81935600-81936800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr16:81935600-81937200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr16:81935600-81937200	ZNF genes & repeats	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links