Variant report

Variant	rs16889349
Chromosome Location	chr6:36948528-36948529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:36948399-36948935	K562	blood:	n/a	n/a
2	POLR2A	chr6:36948492-36949305	K562	blood:	n/a	n/a
3	POLR2A	chr6:36946683-36950240	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:36948480-36949698	K562	blood:	n/a	n/a
5	POLR2A	chr6:36947682-36948664	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36937337..36939324-chr6:36946513..36949209,3	MCF-7	breast:
2	chr6:36937337..36939387-chr6:36947202..36951298,3	MCF-7	breast:
3	chr6:36925903..36928788-chr6:36946034..36948612,2	MCF-7	breast:
4	chr6:36947258..36950041-chr6:36986048..36987573,2	MCF-7	breast:
5	chr6:36859467..36861214-chr6:36946657..36948783,2	MCF-7	breast:
6	chr6:36948207..36949609-chr6:36985741..36986646,4	MCF-7	breast:

No data

Variant related genes	Relation type
MTCH1	TF binding region
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11548576	1.00[JPT][hapmap]
rs11969088	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889318	1.00[JPT][hapmap]
rs16889330	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16889344	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889347	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61748598	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708006	0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs733461	0.87[EUR][1000 genomes]
rs9296204	0.89[GIH][hapmap]
rs9296205	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462264	1.00[CHB][hapmap]
rs9470448	0.87[EUR][1000 genomes]
rs9470449	0.85[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv5263	chr6:36941625-36972109	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic 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	22 gene(s)	inside rSNPs	diseases
5	esv988069	chr6:36942299-36951067	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv518386	chr6:36942746-37037670	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs16889349	CDKN1A	cis	cerebellum	SCAN
rs16889349	PI16	cis	intralobular white matter	BrainEAC
rs16889349	PI16	cis	inferior olivary nucleus	BrainEAC
rs16889349	PI16	cis	parietal	SCAN
rs16889349	PI16	cis	hippocampus	BrainEAC
rs16889349	SRSF3	cis	parietal	SCAN
rs16889349	PI16	cis	cerebellum	SCAN
rs16889349	PI16	cis	brain	BrainEAC
rs16889349	ZFAND3	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36931800-36948600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:36932400-36951800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:36934000-36949600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:36934000-36951600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:36934200-36949200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:36934200-36950400	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr6:36934400-36949200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:36934600-36949200	Strong transcription	Placenta	Placenta
9	chr6:36934800-36949600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr6:36935000-36949800	Genic enhancers	Left Ventricle	heart
11	chr6:36935000-36950200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr6:36935200-36948600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:36936200-36949000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr6:36939000-36951200	Strong transcription	HSMM	muscle
15	chr6:36939400-36949600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:36939600-36948800	Strong transcription	NHEK	skin
17	chr6:36939600-36950600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:36940800-36948600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:36941200-36950600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:36942800-36948800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr6:36944000-36949400	Genic enhancers	Right Ventricle	heart
22	chr6:36945000-36948600	Strong transcription	K562	blood
23	chr6:36945000-36949200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:36945000-36951200	Enhancers	Fetal Heart	heart
25	chr6:36945200-36948600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:36945400-36951400	Weak transcription	Fetal Kidney	kidney
27	chr6:36945600-36948600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:36945600-36949400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr6:36945600-36949800	Genic enhancers	Stomach Smooth Muscle	stomach
30	chr6:36946200-36949000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr6:36946200-36951000	Weak transcription	Small Intestine	intestine
32	chr6:36946200-36952000	Weak transcription	A549	lung
33	chr6:36946400-36948600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:36946400-36948600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:36946400-36948600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:36946400-36948600	Weak transcription	Esophagus	oesophagus
37	chr6:36946400-36948600	Weak transcription	Gastric	stomach
38	chr6:36946400-36949400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:36946400-36949600	Genic enhancers	Fetal Muscle Leg	muscle
40	chr6:36946400-36949800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr6:36946400-36950400	Weak transcription	Ovary	ovary
42	chr6:36946400-36951200	Weak transcription	Hela-S3	cervix
43	chr6:36946400-36951600	Weak transcription	HSMMtube	muscle
44	chr6:36946400-36951800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr6:36946600-36948600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:36946600-36948600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:36946600-36948600	Weak transcription	Aorta	Aorta
48	chr6:36946600-36949200	Weak transcription	Colonic Mucosa	Colon
49	chr6:36946600-36949200	Enhancers	Fetal Lung	lung
50	chr6:36946600-36949600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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