Variant report

Variant	rs12103711
Chromosome Location	chr17:38461640-38461641
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38461106-38462031	GM12892	blood:	n/a	n/a
2	POLR2A	chr17:38460662-38462109	HepG2	liver:	n/a	n/a
3	POLR2A	chr17:38459226-38462021	GM12892	blood:	n/a	n/a
4	POLR2A	chr17:38461516-38462035	K562	blood:	n/a	n/a
5	POLR2A	chr17:38461084-38462071	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr17:38461576-38461995	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr17:38461502-38462026	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr17:38461568-38461873	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr17:38459179-38462046	GM12892	blood:	n/a	n/a
10	POLR2A	chr17:38459064-38462073	K562	blood:	n/a	n/a
11	POLR2A	chr17:38461295-38463015	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr17:38458775-38462061	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr17:38461586-38462016	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr17:38461499-38462039	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr17:38459161-38462037	GM12892	blood:	n/a	n/a
16	POLR2A	chr17:38461525-38462012	K562	blood:	n/a	n/a
17	POLR2A	chr17:38459191-38462034	GM12891	blood:	n/a	n/a
18	POLR2A	chr17:38461549-38462054	HepG2	liver:	n/a	n/a
19	POLR2A	chr17:38461223-38462074	PANC-1	pancreas:	n/a	n/a
20	NFATC1	chr17:38461490-38462078	GM12878	blood:	n/a	n/a
21	POLR2A	chr17:38461505-38461834	K562	blood:	n/a	n/a
22	POLR2A	chr17:38461183-38462024	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:38267756..38269556-chr17:38459898..38462579,2	K562	blood:
2	chr17:38461289..38463378-chr17:38572739..38574780,2	MCF-7	breast:
3	chr17:38461366..38465134-chr17:38511894..38515079,3	K562	blood:
4	chr17:38461085..38463306-chr17:38495562..38499435,4	K562	blood:
5	chr17:38331368..38338782-chr17:38460574..38470405,11	MCF-7	breast:
6	chr17:38461615..38484404-chr17:38597525..38608992,85	MCF-7	breast:

No data

Variant related genes	Relation type
RARA	TF binding region
ENSG00000131747	Chromatin interaction
ENSG00000265666	Chromatin interaction
ENSG00000108352	Chromatin interaction
ENSG00000141753	Chromatin interaction
ENSG00000131759	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12051734	0.93[ASN][1000 genomes]
rs12946680	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13706	0.99[ASN][1000 genomes]
rs1807273	0.92[ASN][1000 genomes]
rs2077464	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2120200	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35286757	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs36030243	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4134994	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs55656553	0.96[ASN][1000 genomes]
rs57179137	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59406133	0.86[ASN][1000 genomes]
rs7217852	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8078226	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9303285	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9303286	0.91[ASN][1000 genomes]
rs9894625	0.91[ASN][1000 genomes]
rs9896312	0.90[ASN][1000 genomes]
rs9904270	0.95[ASN][1000 genomes]
rs9910197	0.85[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058194	chr17:38457226-38502453	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38444800-38462600	Weak transcription	Esophagus	oesophagus
2	chr17:38445600-38462600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:38453000-38462600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:38455800-38462800	Weak transcription	Ovary	ovary
5	chr17:38459000-38461800	Enhancers	NHLF	lung
6	chr17:38459000-38462400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr17:38459000-38465400	Enhancers	Fetal Muscle Leg	muscle
8	chr17:38459000-38465400	Enhancers	Fetal Stomach	stomach
9	chr17:38459200-38462800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr17:38459200-38465200	Enhancers	Fetal Intestine Large	intestine
11	chr17:38459200-38465400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr17:38459200-38473800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr17:38459600-38461800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr17:38459600-38462200	Enhancers	Fetal Muscle Trunk	muscle
15	chr17:38459600-38465200	Enhancers	Placenta	Placenta
16	chr17:38459800-38462600	Weak transcription	Stomach Mucosa	stomach
17	chr17:38459800-38462800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr17:38459800-38462800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr17:38460000-38461800	Weak transcription	Fetal Intestine Small	intestine
20	chr17:38460000-38462600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr17:38460000-38462600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr17:38460000-38462600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr17:38460000-38463200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr17:38460000-38463400	Weak transcription	Primary B cells from cord blood	blood
25	chr17:38460000-38463400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr17:38460000-38464000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr17:38460000-38465200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr17:38460000-38465200	Weak transcription	Brain Angular Gyrus	brain
29	chr17:38460200-38462400	Weak transcription	HepG2	liver
30	chr17:38460200-38462600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr17:38460200-38462600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:38460200-38462600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr17:38460200-38462600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr17:38460200-38462600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr17:38460200-38462800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr17:38460200-38462800	Weak transcription	Colonic Mucosa	Colon
37	chr17:38460200-38463000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr17:38460200-38463600	Weak transcription	Right Ventricle	heart
39	chr17:38460200-38464000	Weak transcription	Brain Hippocampus Middle	brain
40	chr17:38460400-38462400	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr17:38460400-38462600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr17:38460400-38462600	Weak transcription	Thymus	Thymus
43	chr17:38460400-38463200	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr17:38460400-38463400	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr17:38460600-38461800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr17:38460600-38461800	Strong transcription	A549	lung
47	chr17:38460600-38462400	Weak transcription	Primary T cells from cord blood	blood
48	chr17:38460600-38462600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr17:38460600-38462600	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr17:38460600-38462600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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