Variant report

Variant	rs17431717
Chromosome Location	chr12:120912210-120912211
allele	A/G
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	MAX	chr12:120912200-120912832	MCF-7	breast:	n/a	chr12:120912639-120912648
2	SIN3AK20	chr12:120912059-120913006	MCF-7	breast:	n/a	n/a
3	FOXA1	chr12:120912197-120912655	T-47D	breast:	n/a	chr12:120912391-120912403
4	ELF1	chr12:120912172-120912929	HCT-116	colon:	n/a	chr12:120912564-120912577
5	POLR2A	chr12:120912121-120913469	U87	brain:	n/a	n/a
6	GATA3	chr12:120912188-120912803	MCF-7	breast:	n/a	chr12:120912638-120912647 chr12:120912568-120912578
7	JUN	chr12:120912204-120912949	K562	blood:	n/a	chr12:120912639-120912649 chr12:120912640-120912649 chr12:120912643-120912655 chr12:120912639-120912649 chr12:120912639-120912649 chr12:120912639-120912649
8	EP300	chr12:120912188-120912713	T-47D	breast:	n/a	chr12:120912566-120912580 chr12:120912246-120912260 chr12:120912639-120912648
9	FOSL1	chr12:120912166-120912961	HCT-116	colon:	n/a	chr12:120912640-120912649 chr12:120912639-120912649 chr12:120912638-120912649 chr12:120912639-120912649 chr12:120912643-120912655 chr12:120912639-120912649 chr12:120912639-120912649
10	POLR2A	chr12:120912126-120913371	U87	brain:	n/a	n/a
11	SP1	chr12:120912061-120912968	HCT-116	colon:	n/a	n/a
12	TCF7L2	chr12:120911978-120912761	MCF-7	breast:	n/a	chr12:120912140-120912156 chr12:120912141-120912155 chr12:120912143-120912152 chr12:120912144-120912154 chr12:120912640-120912649 chr12:120912144-120912153 chr12:120912140-120912156
13	SIN3AK20	chr12:120912180-120912941	MCF-7	breast:	n/a	n/a
14	JUND	chr12:120912156-120912985	HCT-116	colon:	n/a	chr12:120912639-120912649 chr12:120912640-120912649 chr12:120912643-120912655 chr12:120912639-120912649 chr12:120912639-120912649 chr12:120912639-120912649
15	SIN3AK20	chr12:120912177-120912960	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:120903414..120909393-chr12:120910653..120915482,19	MCF-7	breast:
2	chr12:120727751..120732241-chr12:120903536..120914205,12	MCF-7	breast:
3	chr12:120910777..120912847-chr12:121016682..121018321,2	MCF-7	breast:
4	chr12:120911060..120912767-chr14:53941405..53944319,2	MCF-7	breast:
5	chr12:120903651..120915747-chr12:120930491..120936868,24	K562	blood:
6	chr12:120910390..120913098-chr12:120962746..120965463,2	MCF-7	breast:
7	chr12:120911083..120913950-chr12:120960998..120963373,2	K562	blood:
8	chr12:120899786..120915162-chr12:120926090..120939394,54	MCF-7	breast:
9	chr12:120911190..120915382-chr12:120965465..120968340,3	MCF-7	breast:
10	chr12:120905117..120912400-chr12:120930505..120935641,13	K562	blood:
11	chr12:120874424..120877390-chr12:120911060..120913556,3	MCF-7	breast:
12	chr12:120910734..120913987-chr12:120933079..120935604,5	MCF-7	breast:

Variant related genes	Relation type
SRSF9	TF binding region
ENSG00000111775	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000248008	Chromatin interaction
ENSG00000241030	Chromatin interaction
ENSG00000111780	Chromatin interaction
ENSG00000111786	Chromatin interaction
ENSG00000110871	Chromatin interaction
ENSG00000088986	Chromatin interaction
ENSG00000167272	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10849755	0.93[EUR][1000 genomes]
rs1167695	0.87[EUR][1000 genomes]
rs1167703	0.83[EUR][1000 genomes]
rs1167725	0.93[EUR][1000 genomes]
rs1167726	0.84[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs1167727	0.93[EUR][1000 genomes]
rs12307148	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12310837	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]
rs1614223	0.93[EUR][1000 genomes]
rs1622884	0.85[EUR][1000 genomes]
rs1671767	0.85[EUR][1000 genomes]
rs1671770	0.81[EUR][1000 genomes]
rs1710136	1.00[ASN][1000 genomes]
rs1794748	0.92[EUR][1000 genomes]
rs1794749	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2235222	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4347449	0.82[EUR][1000 genomes]
rs503335	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs550876	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs563920	0.84[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs567156	0.92[EUR][1000 genomes]
rs580016	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588132	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs591992	0.84[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs614226	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs616157	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945873	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs640350	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7137953	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7174	0.84[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs73405622	0.83[EUR][1000 genomes]
rs787824	0.84[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs787827	0.94[EUR][1000 genomes]
rs787832	0.93[EUR][1000 genomes]
rs7956998	0.92[EUR][1000 genomes]
rs7963543	0.84[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7972244	0.92[EUR][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17431717	POP5	cis	cerebellum	SCAN
rs17431717	POP5	cis	lymphoblastoid	seeQTL
rs17431717	HIRA	trans	cerebellum	SCAN
rs17431717	GCN1L1	cis	cerebellum	SCAN
rs17431717	HRK	cis	cerebellum	SCAN
rs17431717	GATC	cis	cerebellum	SCAN
rs17431717	POP5	Cis_1M	lymphoblastoid	RTeQTL
rs17431717	COQ5	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120908200-120933200	Weak transcription	Aorta	Aorta
2	chr12:120908400-120912400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr12:120908400-120912400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr12:120908400-120912400	Weak transcription	Fetal Kidney	kidney
5	chr12:120908400-120912400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr12:120908400-120912400	Weak transcription	NHDF-Ad	bronchial
7	chr12:120908400-120912600	Weak transcription	Brain Anterior Caudate	brain
8	chr12:120908400-120917400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:120908400-120919400	Weak transcription	Right Ventricle	heart
10	chr12:120908400-120919800	Weak transcription	Fetal Intestine Large	intestine
11	chr12:120908400-120925800	Weak transcription	Fetal Intestine Small	intestine
12	chr12:120908400-120926000	Weak transcription	HSMMtube	muscle
13	chr12:120908400-120928800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:120908400-120929000	Weak transcription	Psoas Muscle	Psoas
15	chr12:120908400-120932400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:120908400-120932400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:120908600-120912400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:120908600-120912400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:120908600-120912400	Weak transcription	NHLF	lung
20	chr12:120908600-120912600	Weak transcription	Ovary	ovary
21	chr12:120908600-120917400	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:120908600-120925400	Weak transcription	Pancreas	Pancrea
23	chr12:120908600-120927200	Weak transcription	Fetal Brain Female	brain
24	chr12:120908600-120928200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:120908600-120928600	Weak transcription	Spleen	Spleen
26	chr12:120908600-120928800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:120908600-120932800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:120908600-120932800	Weak transcription	Adipose Nuclei	Adipose
29	chr12:120908600-120932800	Weak transcription	Brain Germinal Matrix	brain
30	chr12:120908600-120932800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr12:120908600-120933000	Weak transcription	Thymus	Thymus
32	chr12:120908800-120917400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:120908800-120926000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr12:120908800-120928400	Weak transcription	Primary T cells from cord blood	blood
35	chr12:120909000-120912400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr12:120909200-120914200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr12:120909200-120919400	Weak transcription	Fetal Stomach	stomach
38	chr12:120909200-120919600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr12:120909400-120912400	Weak transcription	Stomach Mucosa	stomach
40	chr12:120909600-120913600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:120910400-120913800	Enhancers	Placenta Amnion	Placenta Amnion
42	chr12:120910600-120913200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:120910600-120917400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr12:120910800-120912400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:120911000-120912800	Enhancers	Placenta	Placenta
46	chr12:120911000-120913800	Enhancers	K562	blood
47	chr12:120911000-120917400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr12:120911000-120932800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:120911600-120912800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:120911600-120912800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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