Variant report

Variant	rs16948168
Chromosome Location	chr12:118602681-118602682
allele	C/T
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	POLR2A	chr12:118601679-118605628	K562	blood:	n/a	n/a
2	CTCF	chr12:118602560-118602710	NHLF	lung:	n/a	n/a
3	RAD21	chr12:118602653-118603411	SK-N-SH	brain:	n/a	chr12:118603008-118603027
4	CTCF	chr12:118602671-118603302	HCT-116	colon:	n/a	chr12:118603007-118603025 chr12:118603009-118603030
5	ZKSCAN1	chr12:118602607-118603143	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr12:118602600-118602750	HCFaa	heart:	n/a	n/a
7	CTCF	chr12:118602438-118603425	A549	lung:	n/a	chr12:118603007-118603025 chr12:118603009-118603030

No.	Distal block	Cell Line	Cell type
1	chr12:118596811..118599066-chr12:118602668..118604454,2	MCF-7	breast:
2	chr12:118602518..118604035-chr12:118606751..118609682,2	MCF-7	breast:
3	chr12:118602460..118604625-chr12:118813262..118815515,3	MCF-7	breast:
4	chr12:118601731..118605413-chr12:118811549..118815749,6	MCF-7	breast:
5	chr12:118491454..118494389-chr12:118600464..118603193,2	K562	blood:
6	chr12:118598981..118601040-chr12:118601052..118602863,2	MCF-7	breast:
7	chr12:118602638..118603497-chr12:118815737..118816345,4	MCF-7	breast:
8	chr12:118558430..118559056-chr12:118602563..118603381,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221280	TF binding region
TAOK3	TF binding region
ENSG00000176834	Chromatin interaction
ENSG00000111707	Chromatin interaction
ENSG00000135090	Chromatin interaction
ENSG00000270482	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10507288	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs16948163	1.00[AMR][1000 genomes]
rs16948171	1.00[AMR][1000 genomes]
rs16948173	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948189	1.00[AMR][1000 genomes]
rs16948193	0.80[YRI][hapmap]
rs16948195	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948199	0.86[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948224	0.86[YRI][hapmap]
rs16948225	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs16948241	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs16948245	1.00[AMR][1000 genomes]
rs16948258	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs16948259	1.00[AMR][1000 genomes]
rs16948262	1.00[AMR][1000 genomes]
rs17433259	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs17440336	0.86[YRI][hapmap]
rs17440364	0.86[YRI][hapmap]
rs17512177	0.83[YRI][hapmap]
rs17512198	0.86[YRI][hapmap]
rs55965100	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56210304	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56319724	1.00[AMR][1000 genomes]
rs56743940	1.00[AMR][1000 genomes]
rs56802741	1.00[AMR][1000 genomes]
rs56819745	1.00[AMR][1000 genomes]
rs57072278	1.00[AMR][1000 genomes]
rs57170485	1.00[AMR][1000 genomes]
rs5745863	1.00[AMR][1000 genomes]
rs57865918	1.00[AMR][1000 genomes]
rs58340234	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58797246	1.00[AMR][1000 genomes]
rs59036425	1.00[AMR][1000 genomes]
rs59151662	1.00[AMR][1000 genomes]
rs59360632	1.00[AMR][1000 genomes]
rs59558138	1.00[AMR][1000 genomes]
rs60160994	1.00[AMR][1000 genomes]
rs60917706	1.00[AMR][1000 genomes]
rs7962185	0.80[YRI][hapmap]
rs7963735	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs7963880	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs7965350	0.80[YRI][hapmap]
rs7977168	0.86[AFR][1000 genomes];1.00[AMR][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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1054703	chr12:118575000-118638613	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv541611	chr12:118575000-118638613	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1035497	chr12:118599539-118732144	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv541612	chr12:118599539-118732144	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118576000-118619600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr12:118576000-118624000	Weak transcription	Stomach Mucosa	stomach
3	chr12:118578200-118611600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:118578600-118603200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:118584000-118627600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:118585600-118603000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:118585800-118619000	Weak transcription	HepG2	liver
8	chr12:118586200-118619400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:118586600-118613600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:118586800-118603600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:118587600-118611200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:118587600-118619200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:118587800-118620000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:118589600-118619000	Weak transcription	A549	lung
15	chr12:118590400-118617000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:118592600-118619400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:118593200-118619200	Strong transcription	Fetal Brain Female	brain
18	chr12:118593200-118619400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:118593200-118619600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr12:118598200-118620000	Weak transcription	Hela-S3	cervix
21	chr12:118599000-118607800	Weak transcription	Fetal Brain Male	brain
22	chr12:118599200-118608000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr12:118599400-118607200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:118599600-118604800	Weak transcription	NH-A	brain
25	chr12:118599600-118605600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr12:118599800-118607400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:118599800-118607600	Weak transcription	Small Intestine	intestine
28	chr12:118599800-118608000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:118599800-118608200	Weak transcription	Colonic Mucosa	Colon
30	chr12:118599800-118608200	Weak transcription	HMEC	breast
31	chr12:118599800-118608400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:118599800-118608400	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:118599800-118609800	Weak transcription	Psoas Muscle	Psoas
34	chr12:118599800-118609800	Weak transcription	HUVEC	blood vessel
35	chr12:118599800-118613000	Weak transcription	HSMMtube	muscle
36	chr12:118599800-118625600	Weak transcription	Pancreas	Pancrea
37	chr12:118600000-118603000	Weak transcription	GM12878-XiMat	blood
38	chr12:118600000-118603200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:118600000-118604800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:118600000-118605400	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:118600000-118605800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:118600000-118605800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:118600000-118607200	Weak transcription	Esophagus	oesophagus
44	chr12:118600000-118607200	Weak transcription	Fetal Intestine Small	intestine
45	chr12:118600000-118607400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr12:118600000-118607800	Weak transcription	Spleen	Spleen
47	chr12:118600000-118608000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr12:118600000-118608000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:118600000-118608800	Weak transcription	Gastric	stomach
50	chr12:118600000-118609400	Weak transcription	Right Ventricle	heart

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