Variant report

Variant	rs12310837
Chromosome Location	chr12:120880572-120880573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:120880391-120880986	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr12:120880459-120880761	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:120880337-120880736	K562	blood:	n/a	n/a
4	POLR2A	chr12:120880499-120881336	K562	blood:	n/a	n/a
5	POLR2A	chr12:120880384-120881396	GM12892	blood:	n/a	n/a
6	POLR2A	chr12:120880338-120884699	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr12:120880460-120881395	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:120880536-120881004	MCF-7	breast:	n/a	n/a
9	POLR2A	chr12:120880507-120881362	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:120880564-120880799	HCT-116	colon:	n/a	n/a
11	POLR2A	chr12:120880522-120880631	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr12:120880378-120881281	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr12:120880480-120881636	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:120880530-120880612	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr12:120880216-120881309	PFSK-1	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:120880522-120880572	HIPEpiC	eye:	n/a
2	chr12:120880522-120880572	GM12878	blood:	n/a
3	chr12:120880522-120880572	GM12891	blood:	n/a
4	chr12:120880522-120880572	HL-60	blood:	n/a
5	chr12:120880522-120880572	HEK293	kidney:	embryo
6	chr12:120880522-120880572	HNPCEpiC	eye:	n/a
7	chr12:120880522-120880572	HCM	heart:	n/a
8	chr12:120880522-120880572	CMK	blood:	n/a
9	chr12:120880522-120880572	ProgFib	skin:	n/a
10	chr12:120880522-120880572	HRE	kidney:	n/a
11	chr12:120880522-120880572	A549	lung:	n/a
12	chr12:120880522-120880572	NHBE	bronchial:	n/a
13	chr12:120880522-120880572	NH-A	brain:	n/a
14	chr12:120880522-120880572	BE2_C	brain:	n/a
15	chr12:120880522-120880572	GM19239	blood:	n/a
16	chr12:120880522-120880572	GM12892	blood:	n/a
17	chr12:120880522-120880572	AG09319	gingival:	n/a
18	chr12:120880522-120880572	HEEpiC	esophagus:	n/a
19	chr12:120880522-120880572	PrEC	prostate:	n/a
20	chr12:120880522-120880572	SKMC	muscle:	n/a
21	chr12:120880522-120880572	U87	brain:	n/a
22	chr12:120880522-120880572	SK-N-SH_RA	brain:	n/a
23	chr12:120880522-120880572	HUVEC	blood vessel:	n/a
24	chr12:120880522-120880572	HAEpiC	amniotic membrane:	n/a
25	chr12:120880522-120880572	HCPEpiC	choroid plexus:	n/a
26	chr12:120880522-120880572	MCF-7	breast:	n/a
27	chr12:120880522-120880572	AoSMC	blood vessel:	n/a
28	chr12:120880522-120880572	HCT-116	colon:	n/a
29	chr12:120880522-120880572	T-47D	breast:	n/a
30	chr12:120880522-120880572	SK-N-SH	brain:	n/a
31	chr12:120880522-120880572	Hepatocyte	liver:	n/a
32	chr12:120880522-120880572	SAEC	small airway:	n/a
33	chr12:120880522-120880572	ovcar-3	ovarian:	n/a
34	chr12:120880522-120880572	K562	blood:	n/a
35	chr12:120880522-120880572	HMEC	breast:	n/a
36	chr12:120880522-120880572	HRCEpiC	kidney:	n/a
37	chr12:120880522-120880572	AG10803	skin:	n/a
38	chr12:120880522-120880572	HRPEpiC	eye:	n/a
39	chr12:120880522-120880572	Hela-S3	cervix:	n/a
40	chr12:120880522-120880572	ECC-1	luminal epithelium:	n/a
41	chr12:120880522-120880572	LNCaP	prostate:	n/a
42	chr12:120880522-120880572	Caco-2	colon:	n/a
43	chr12:120880522-120880572	RPTEC	kidney:	n/a
44	chr12:120880522-120880572	AG09309	skin:	n/a
45	chr12:120880522-120880572	NT2-D1	testis:	n/a
46	chr12:120880522-120880572	MCF10A-Er-Src	breast:	n/a
47	chr12:120880522-120880572	PFSK-1	brain:	n/a
48	chr12:120880522-120880572	IMR90	lung:	fetal
49	chr12:120880522-120880572	NB4	blood:	n/a
50	chr12:120880522-120880572	AG04450	lung:	fetal

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

No.	Distal block	Cell Line	Cell type
1	chr12:120728088..120729982-chr12:120880353..120882117,2	K562	blood:
2	chr12:120879804..120882085-chr12:120900465..120903221,2	K562	blood:
3	chr12:120880538..120882085-chr12:120906058..120908502,2	MCF-7	breast:
4	chr12:120728284..120732232-chr12:120880260..120886911,13	MCF-7	breast:
5	chr12:120879789..120885007-chr12:120906681..120910772,6	K562	blood:

No data

Variant related genes	Relation type
GATC	TF binding region
GATC	CpG island
ENSG00000088986	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000111786	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10849755	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1167695	0.81[EUR][1000 genomes]
rs1167725	0.86[EUR][1000 genomes]
rs1167726	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1167727	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12307148	0.87[EUR][1000 genomes]
rs1614223	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1710136	1.00[ASN][1000 genomes]
rs17431717	0.81[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794748	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1794749	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2235222	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs503335	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs550876	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs563920	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs567156	0.85[EUR][1000 genomes]
rs580016	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588132	1.00[CEU][hapmap]
rs591992	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs614226	0.81[ASW][hapmap];1.00[CEU][hapmap];0.84[LWK][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs616157	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945858	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61945873	0.82[EUR][1000 genomes]
rs640350	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7137953	0.84[CEU][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs7174	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs787824	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs787827	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs787832	0.86[EUR][1000 genomes]
rs7956998	0.85[EUR][1000 genomes]
rs7963543	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7972244	0.85[EUR][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	nsv819389	chr12:120880098-120882476	Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12310837	POP5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120876400-120883400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:120876800-120881800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:120876800-120883400	Weak transcription	Esophagus	oesophagus
4	chr12:120877000-120880600	Weak transcription	Aorta	Aorta
5	chr12:120877000-120881200	Weak transcription	Psoas Muscle	Psoas
6	chr12:120877000-120883000	Weak transcription	Pancreas	Pancrea
7	chr12:120877000-120883200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:120877200-120881000	Weak transcription	Gastric	stomach
9	chr12:120877200-120882000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:120877200-120882000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:120877200-120883000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:120877200-120883200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:120877400-120880600	Weak transcription	Right Ventricle	heart
14	chr12:120877400-120882800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr12:120877600-120880600	Weak transcription	NHLF	lung
16	chr12:120877800-120882000	Strong transcription	Fetal Stomach	stomach
17	chr12:120877800-120882200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:120877800-120882600	Strong transcription	Left Ventricle	heart
19	chr12:120877800-120883400	Weak transcription	Stomach Mucosa	stomach
20	chr12:120878000-120881800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:120878000-120881800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:120878000-120882000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:120878000-120882000	Weak transcription	NH-A	brain
24	chr12:120878000-120882200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:120878000-120882400	Strong transcription	Primary B cells from peripheral blood	blood
26	chr12:120878000-120882600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:120878000-120882600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:120878000-120882600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr12:120878000-120882600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:120878000-120882600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:120878000-120882600	Strong transcription	Placenta	Placenta
32	chr12:120878000-120882600	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr12:120878000-120882600	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr12:120878000-120882800	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:120878000-120882800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:120878000-120882800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr12:120878000-120882800	Strong transcription	Fetal Thymus	thymus
38	chr12:120878000-120883000	Strong transcription	Fetal Muscle Leg	muscle
39	chr12:120878000-120883200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:120878000-120883200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:120878000-120883200	Weak transcription	Fetal Brain Male	brain
42	chr12:120878000-120883200	Weak transcription	Right Atrium	heart
43	chr12:120878000-120883400	Weak transcription	Small Intestine	intestine
44	chr12:120878200-120880600	Weak transcription	Primary B cells from cord blood	blood
45	chr12:120878200-120881600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr12:120878200-120881600	Strong transcription	Dnd41	blood
47	chr12:120878200-120881800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:120878200-120881800	Strong transcription	K562	blood
49	chr12:120878200-120882000	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr12:120878200-120882000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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