Variant report

Variant	rs1641850
Chromosome Location	chr16:12188433-12188434
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr16:12188370-12188570	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr16:12188300-12188450	GM12865	blood:	n/a	n/a
3	CTCF	chr16:12188300-12188450	BE2_C	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12183674..12186424-chr16:12186757..12189168,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175604	TF binding region
ENSG00000175604	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1641855	0.83[EUR][1000 genomes]
rs168414	0.85[EUR][1000 genomes]
rs1704112	0.83[EUR][1000 genomes]
rs1704116	0.82[EUR][1000 genomes]
rs17216341	1.00[JPT][hapmap]
rs17805158	1.00[JPT][hapmap];0.81[LWK][hapmap]
rs183008	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs193252	0.85[EUR][1000 genomes]
rs2664186	0.83[EUR][1000 genomes]
rs350203	0.82[EUR][1000 genomes]
rs350207	0.83[EUR][1000 genomes]
rs350209	0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs350210	0.83[EUR][1000 genomes]
rs350226	0.84[AMR][1000 genomes]
rs350231	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350232	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350245	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs350248	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs350251	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs350252	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs350254	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs350255	0.82[EUR][1000 genomes]
rs350256	0.82[EUR][1000 genomes]
rs350271	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs350274	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs350275	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs350277	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs350278	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs350279	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs350285	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs350287	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4781187	0.83[AMR][1000 genomes]
rs9922788	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv977111	chr16:12161129-12220593	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1039492	chr16:12176517-12210702	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv571460	chr16:12181702-12238602	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1052973	chr16:12188092-12307880	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1641850	PARN	cis	cerebellum	SCAN
rs1641850	PRM2	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12142800-12189200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr16:12178600-12199600	Weak transcription	Aorta	Aorta
3	chr16:12182200-12188600	Weak transcription	Fetal Brain Male	brain
4	chr16:12183800-12189200	Weak transcription	Pancreas	Pancrea
5	chr16:12184000-12189000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr16:12184000-12189200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr16:12184000-12189200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr16:12184000-12189200	Weak transcription	Liver	Liver
9	chr16:12184000-12189200	Weak transcription	Colon Smooth Muscle	Colon
10	chr16:12184000-12189200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr16:12184000-12189400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr16:12184000-12191600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr16:12184200-12189000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr16:12184200-12189000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr16:12184200-12189200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr16:12184200-12189200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr16:12184200-12189200	Weak transcription	Fetal Intestine Large	intestine
18	chr16:12184200-12190400	Enhancers	Thymus	Thymus
19	chr16:12184200-12192200	Weak transcription	Gastric	stomach
20	chr16:12184200-12193000	Enhancers	Fetal Thymus	thymus
21	chr16:12184400-12189200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr16:12184400-12231200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr16:12184600-12188800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr16:12184600-12188800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr16:12184600-12189200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr16:12185400-12189000	Strong transcription	Primary B cells from cord blood	blood
27	chr16:12185400-12189200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr16:12186000-12188800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr16:12186000-12189800	Weak transcription	Esophagus	oesophagus
30	chr16:12186200-12189200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr16:12186400-12189400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr16:12186600-12188800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr16:12186600-12188800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr16:12186600-12188800	Weak transcription	Fetal Stomach	stomach
35	chr16:12186600-12188800	Weak transcription	K562	blood
36	chr16:12186600-12189200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr16:12186600-12189200	Weak transcription	A549	lung
38	chr16:12186600-12189400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr16:12186600-12189400	Weak transcription	Fetal Kidney	kidney
40	chr16:12186600-12189800	Weak transcription	Small Intestine	intestine
41	chr16:12186600-12190800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr16:12186600-12190800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr16:12186800-12188600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr16:12186800-12188600	Weak transcription	Fetal Lung	lung
45	chr16:12186800-12188800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr16:12186800-12188800	Weak transcription	Brain Angular Gyrus	brain
47	chr16:12186800-12188800	Weak transcription	Brain Anterior Caudate	brain
48	chr16:12186800-12188800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr16:12186800-12188800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr16:12186800-12189000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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