Variant report

Variant	rs12981698
Chromosome Location	chr19:36619392-36619393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:36618599..36619476-chr3:186523865..186524409,2	HCT-116	colon:
2	chr19:36618000..36620412-chr19:36704144..36708307,3	K562	blood:
3	chr19:36618936..36620566-chr19:36620843..36623517,2	MCF-7	breast:
4	chr1:155164726..155165363-chr19:36619081..36619616,2	Hela-S3	cervix:
5	chr19:36619003..36619532-chr21:44846275..44846905,2	Hela-S3	cervix:
6	chr19:36615077..36620423-chr19:36622100..36624907,6	K562	blood:
7	chr19:36618937..36619527-chr3:50374881..50375586,2	Hela-S3	cervix:
8	chr19:36617317..36620455-chr19:36659858..36661867,3	MCF-7	breast:
9	chr19:36618747..36620839-chr19:36626381..36628843,2	K562	blood:
10	chr19:36618864..36621054-chr19:36633673..36635614,2	MCF-7	breast:
11	chr19:36617223..36621168-chr19:36621174..36623571,4	MCF-7	breast:
12	chr19:36616979..36620071-chr19:36629993..36632800,4	K562	blood:
13	chr19:36548167..36550367-chr19:36618997..36621964,2	MCF-7	breast:
14	chr19:36618571..36620439-chr19:36630618..36633612,4	K562	blood:
15	chr19:36607813..36612546-chr19:36618709..36622770,5	MCF-7	breast:
16	chr19:36544760..36547180-chr19:36619218..36620839,2	MCF-7	breast:
17	chr19:36604546..36607360-chr19:36618768..36621055,2	MCF-7	breast:
18	chr19:36617250..36625256-chr19:36625801..36633837,31	MCF-7	breast:
19	chr19:36612874..36616073-chr19:36617819..36620812,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBCB-2	chr19:36618669-36620042	NONHSAT065959

No data

Variant related genes	Relation type
ENSG00000196357	Chromatin interaction
ENSG00000161277	Chromatin interaction
ENSG00000105258	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000075702	Chromatin interaction
ENSG00000271748	Chromatin interaction
ENSG00000167635	Chromatin interaction
ENSG00000068028	Chromatin interaction
ENSG00000163918	Chromatin interaction
ENSG00000105254	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1009381	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10406862	1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap]
rs10418079	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10419924	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10420345	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10421377	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10422055	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10425700	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs11669890	0.92[CHB][hapmap];0.86[CHD][hapmap]
rs11879369	0.92[EUR][1000 genomes]
rs12462159	1.00[CHB][hapmap]
rs12608517	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[YRI][hapmap]
rs12971639	0.95[EUR][1000 genomes]
rs12971936	0.97[EUR][1000 genomes]
rs12972828	0.95[EUR][1000 genomes]
rs2023866	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2051800	0.82[MKK][hapmap]
rs2072605	0.82[CEU][hapmap]
rs2074435	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2075472	0.93[CHB][hapmap];0.83[CHD][hapmap]
rs2141959	0.85[ASN][1000 genomes]
rs2227260	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2231568	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2301734	1.00[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs2301737	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs2871649	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs3810447	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4555271	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[YRI][hapmap];0.85[ASN][1000 genomes]
rs4806249	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap]
rs4806254	1.00[CHB][hapmap];0.90[YRI][hapmap]
rs4806262	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4806273	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4806276	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[YRI][hapmap]
rs6510516	0.80[YRI][hapmap]
rs7251912	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7257026	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7258807	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[YRI][hapmap]
rs8104047	0.93[EUR][1000 genomes]
rs8104053	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12981698	PHLDB3	cis	parietal	SCAN
rs12981698	LOC390940	cis	parietal	SCAN
rs12981698	POLR2I///RPSA	Cis_1M	lymphoblastoid	RTeQTL
rs12981698	CYP2A7	cis	parietal	SCAN
rs12981698	PSG9	cis	cerebellum	SCAN
rs12981698	CYP2A7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36617200-36619400	Weak transcription	Gastric	stomach
2	chr19:36618400-36619400	Active TSS	Colon Smooth Muscle	Colon
3	chr19:36618400-36619400	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr19:36618400-36619400	Active TSS	Right Ventricle	heart
5	chr19:36618400-36619400	Active TSS	NHLF	lung
6	chr19:36618400-36619800	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr19:36618400-36619800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:36618400-36619800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:36618400-36619800	Active TSS	Esophagus	oesophagus
10	chr19:36618400-36619800	Active TSS	Fetal Kidney	kidney
11	chr19:36618400-36619800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr19:36618400-36620000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr19:36618400-36621000	Enhancers	Stomach Mucosa	stomach
14	chr19:36618600-36619400	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr19:36618600-36619400	Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr19:36618600-36619400	Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr19:36618600-36619400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:36618600-36619400	Active TSS	Brain Cingulate Gyrus	brain
19	chr19:36618600-36619400	Active TSS	Brain Hippocampus Middle	brain
20	chr19:36618600-36619400	Active TSS	Left Ventricle	heart
21	chr19:36618600-36619600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr19:36618600-36619600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr19:36618600-36619600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:36618600-36619600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:36618600-36619600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:36618600-36619600	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr19:36618600-36619600	Active TSS	Psoas Muscle	Psoas
28	chr19:36618600-36619600	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr19:36618600-36619800	Active TSS	H9 Cell Line	embryonic stem cell
30	chr19:36618600-36619800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:36618600-36619800	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr19:36618600-36619800	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr19:36618600-36619800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr19:36618600-36619800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:36618600-36619800	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr19:36618600-36619800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:36618600-36619800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:36618600-36619800	Flanking Active TSS	Fetal Muscle Trunk	muscle
39	chr19:36618600-36619800	Active TSS	Right Atrium	heart
40	chr19:36618600-36619800	Active TSS	HSMMtube	muscle
41	chr19:36618600-36620000	Active TSS	H1 Cell Line	embryonic stem cell
42	chr19:36618600-36620000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:36618600-36620000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:36618600-36620000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr19:36618600-36620000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:36618600-36620000	Enhancers	Spleen	Spleen
47	chr19:36618600-36620200	Active TSS	HepG2	liver
48	chr19:36618600-36620400	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr19:36618800-36619400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:36618800-36619400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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