Variant report

Variant	rs12335532
Chromosome Location	chr9:96193955-96193956
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	GATA3	chr9:96193750-96194054	MCF-7	breast:	n/a	n/a
2	MAFK	chr9:96193882-96194318	K562	blood:	n/a	chr9:96194150-96194167 chr9:96194158-96194169 chr9:96194159-96194170 chr9:96194154-96194170 chr9:96194157-96194171 chr9:96194154-96194169 chr9:96194159-96194170
3	GATA3	chr9:96193834-96194110	MCF-7	breast:	n/a	n/a
4	HNF4A	chr9:96193771-96194075	HepG2	liver:	n/a	chr9:96193959-96193977 chr9:96193962-96193974 chr9:96193961-96193974 chr9:96193962-96193974 chr9:96193961-96193975 chr9:96193960-96193975 chr9:96193960-96193975 chr9:96193960-96193975
5	HNF4A	chr9:96193840-96194120	HepG2	liver:	n/a	chr9:96193959-96193977 chr9:96193962-96193974 chr9:96193961-96193974 chr9:96193962-96193974 chr9:96193961-96193975 chr9:96193960-96193975 chr9:96193960-96193975 chr9:96193960-96193975
6	SIN3AK20	chr9:96193620-96194244	MCF-7	breast:	n/a	n/a
7	BHLHE40	chr9:96193930-96194262	HepG2	liver:	n/a	n/a
8	GATA3	chr9:96193665-96194316	MCF-7	breast:	n/a	n/a
9	GATA3	chr9:96193486-96194405	MCF-7	breast:	n/a	n/a
10	FOXA1	chr9:96193646-96194077	HepG2	liver:	n/a	n/a
11	MYC	chr9:96193842-96194231	K562	blood:	n/a	n/a
12	ELF1	chr9:96193719-96194492	MCF-7	breast:	n/a	chr9:96194201-96194214 chr9:96194203-96194214 chr9:96194227-96194240
13	GATA3	chr9:96193711-96194071	T-47D	breast:	n/a	n/a
14	BHLHE40	chr9:96193824-96194318	K562	blood:	n/a	n/a
15	POLR2A	chr9:96193900-96194007	MCF10A-Er-Src	breast:	n/a	n/a
16	MAFK	chr9:96193865-96194772	HepG2	liver:	n/a	chr9:96194150-96194167 chr9:96194158-96194169 chr9:96194159-96194170 chr9:96194154-96194170 chr9:96194157-96194171 chr9:96194154-96194169 chr9:96194159-96194170
17	FOXA2	chr9:96193765-96194070	HepG2	liver:	n/a	n/a
18	GATA3	chr9:96193692-96194107	T-47D	breast:	n/a	n/a
19	FOXA1	chr9:96193708-96194114	T-47D	breast:	n/a	n/a
20	FOXA1	chr9:96193746-96194044	T-47D	breast:	n/a	n/a
21	ZNF217	chr9:96193805-96194115	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:96054744..96057085-chr9:96193778..96195427,2	MCF-7	breast:
2	chr9:96193866..96195671-chr9:96205217..96208189,2	K562	blood:
3	chr9:96193694..96195891-chr9:96211466..96214118,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM120A-2	chr9:96193447-96194991	NONHSAT133251

Variant related genes	Relation type
ENSG00000237385	TF binding region
ENSG00000165238	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000188938	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12554020	0.81[CEU][hapmap]
rs12555047	0.84[EUR][1000 genomes]
rs3815563	0.91[CEU][hapmap]
rs3933796	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3933797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4552973	0.82[CEU][hapmap]
rs55766809	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7853605	0.91[CEU][hapmap];0.86[GIH][hapmap]
rs7859267	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12335532	RP11-165J3.6	cis	Skin Sun Exposed Lower leg	GTEx
rs12335532	RP11-165J3.6	cis	Thyroid	GTEx
rs12335532	MYOT	trans	brain	seeQTL
rs12335532	ANKRD19	cis	cerebellum	SCAN
rs12335532	PHF16	trans	brain	seeQTL
rs12335532	RP11-165J3.6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96185800-96208200	Weak transcription	Gastric	stomach
2	chr9:96186000-96208200	Weak transcription	Pancreas	Pancrea
3	chr9:96186600-96208200	Weak transcription	Lung	lung
4	chr9:96190600-96196600	Weak transcription	Placenta	Placenta
5	chr9:96192600-96194200	Weak transcription	Spleen	Spleen
6	chr9:96193000-96196600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:96193200-96194400	Enhancers	Fetal Intestine Large	intestine
8	chr9:96193800-96194000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:96193800-96194000	Enhancers	Thymus	Thymus
10	chr9:96193800-96194200	Enhancers	Duodenum Mucosa	Duodenum
11	chr9:96193800-96194400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:96193800-96194400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:96193800-96194400	Enhancers	Fetal Intestine Small	intestine
14	chr9:96193800-96194400	Enhancers	Fetal Kidney	kidney
15	chr9:96193800-96194400	Enhancers	Small Intestine	intestine
16	chr9:96193800-96194400	Flanking Active TSS	HepG2	liver
17	chr9:96193800-96194400	Enhancers	K562	blood
18	chr9:96193800-96194800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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