Variant report

Variant	rs4439990
Chromosome Location	chr2:191398353-191398354
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr2:191398237-191399549	GM12878	blood:	n/a	chr2:191398742-191398753
2	JUND	chr2:191398341-191398697	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr2:191398351-191399847	GM12878	blood:	n/a	n/a
4	CHD1	chr2:191397854-191400364	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:191398303-191400063	GM12892	blood:	n/a	n/a
6	POLR2A	chr2:191398318-191400015	GM12892	blood:	n/a	n/a
7	JUND	chr2:191398148-191399030	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:191398256-191400006	Raji	blood:	n/a	n/a
9	RUNX3	chr2:191398117-191399964	GM12878	blood:	n/a	n/a
10	MAX	chr2:191398277-191400033	NB4	blood:	n/a	chr2:191399561-191399571
11	POLR2A	chr2:191397873-191400077	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:191398214-191399817	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:191398158-191399977	GM12878	blood:	n/a	n/a
14	RELA	chr2:191398239-191399896	GM19099	blood:	n/a	n/a
15	RELA	chr2:191398303-191399837	GM15510	blood:	n/a	n/a
16	HEY1	chr2:191398232-191399944	HepG2	liver:	n/a	n/a
17	POLR2A	chr2:191398290-191400473	Hela-S3	cervix:	n/a	n/a
18	JUN	chr2:191398161-191398456	HepG2	liver:	n/a	chr2:191398312-191398325
19	POLR2A	chr2:191398309-191399932	GM18951	blood:	n/a	n/a
20	GATA1	chr2:191398203-191399917	PBDE	blood:	n/a	n/a
21	WRNIP1	chr2:191398204-191399133	GM12878	blood:	n/a	n/a
22	JUND	chr2:191398137-191398489	K562	blood:	n/a	n/a
23	MBD4	chr2:191398196-191400004	HepG2	liver:	n/a	n/a
24	RCOR1	chr2:191397897-191398477	K562	blood:	n/a	n/a
25	POLR2A	chr2:191398273-191399994	HepG2	liver:	n/a	n/a
26	PML	chr2:191398307-191400151	GM12878	blood:	n/a	chr2:191399462-191399470
27	MYBL2	chr2:191398345-191399922	HepG2	liver:	n/a	n/a
28	POLR2A	chr2:191398313-191399946	GM19099	blood:	n/a	n/a
29	POLR2A	chr2:191397202-191400008	GM12878	blood:	n/a	n/a
30	MTA3	chr2:191398209-191399201	GM12878	blood:	n/a	n/a
31	MTA3	chr2:191397701-191400798	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:191398122-191399899	U87	brain:	n/a	n/a
33	POLR2A	chr2:191397141-191400056	GM12891	blood:	n/a	n/a
34	CEBPB	chr2:191398327-191399334	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:191397602..191400323-chr2:191511853..191515845,7	MCF-7	breast:
2	chr2:191397324..191399612-chr2:191415383..191418342,2	MCF-7	breast:
3	chr2:191397736..191401145-chr2:191512338..191515436,3	K562	blood:
4	chr2:191271812..191274120-chr2:191398223..191400840,2	K562	blood:
5	chr2:191385869..191388991-chr2:191394619..191398567,3	K562	blood:
6	chr2:191389345..191393382-chr2:191397304..191400533,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000233654	TF binding region
ENSG00000251935	Chromatin interaction
ENSG00000189362	Chromatin interaction
ENSG00000138386	Chromatin interaction
ENSG00000151690	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10174174	0.81[ASN][1000 genomes]
rs10188341	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs10190082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10197348	0.95[JPT][hapmap]
rs10432434	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10931458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1128723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11885992	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12052514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12053190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12470863	0.82[ASN][1000 genomes]
rs12472081	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12477369	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12693579	0.95[ASN][1000 genomes]
rs13417431	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16832765	0.81[CEU][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2192010	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35818159	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4129082	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs4258824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4261750	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs4287794	0.88[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4340549	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4371384	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4641969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4853510	0.97[ASN][1000 genomes]
rs4853710	0.89[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4853713	0.89[CHB][hapmap]
rs4853716	0.96[ASN][1000 genomes]
rs56127319	0.81[EUR][1000 genomes]
rs56342910	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58568707	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59929070	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60915953	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61709084	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62180992	0.80[ASN][1000 genomes]
rs62181018	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62181019	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62181020	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62181029	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62181034	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62181052	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62182865	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62182885	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62182897	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6711928	0.80[ASN][1000 genomes]
rs6712426	0.96[ASN][1000 genomes]
rs6727669	0.96[ASN][1000 genomes]
rs6731287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7567059	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7569128	0.86[CEU][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7581762	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs7581986	0.84[CHB][hapmap];0.95[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4439990	INPP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191375200-191398600	Weak transcription	Ovary	ovary
2	chr2:191382600-191398400	Weak transcription	Psoas Muscle	Psoas
3	chr2:191387400-191398600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:191391200-191398400	Weak transcription	Small Intestine	intestine
5	chr2:191391200-191398600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:191393200-191398600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:191393400-191398600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:191393400-191398600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:191393400-191398600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:191393600-191398400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:191393600-191398600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:191393800-191398400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:191394800-191398400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:191394800-191398600	Weak transcription	Esophagus	oesophagus
15	chr2:191394800-191398600	Weak transcription	Gastric	stomach
16	chr2:191395200-191398400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:191395200-191398400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:191395400-191398400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:191395400-191398400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:191395400-191398400	Weak transcription	NH-A	brain
21	chr2:191395400-191398600	Weak transcription	HSMMtube	muscle
22	chr2:191395600-191398400	Weak transcription	Brain Anterior Caudate	brain
23	chr2:191395600-191398400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:191395600-191398400	Weak transcription	Lung	lung
25	chr2:191395600-191398400	Weak transcription	Hela-S3	cervix
26	chr2:191395600-191398400	Weak transcription	HSMM	muscle
27	chr2:191395600-191398400	Weak transcription	NHDF-Ad	bronchial
28	chr2:191395600-191398600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:191395800-191398400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:191395800-191398400	Weak transcription	Stomach Mucosa	stomach
31	chr2:191396200-191398400	Weak transcription	Fetal Intestine Small	intestine
32	chr2:191396200-191398400	Weak transcription	Right Atrium	heart
33	chr2:191396200-191398400	Weak transcription	Right Ventricle	heart
34	chr2:191396200-191398600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:191396200-191398600	Weak transcription	Left Ventricle	heart
36	chr2:191397000-191398400	Enhancers	HMEC	breast
37	chr2:191397000-191398600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:191397000-191398600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr2:191397200-191398600	Enhancers	Fetal Heart	heart
40	chr2:191397400-191398400	Weak transcription	Aorta	Aorta
41	chr2:191397400-191398400	Enhancers	Liver	Liver
42	chr2:191397400-191398400	Enhancers	Fetal Muscle Leg	muscle
43	chr2:191397400-191398600	Flanking Active TSS	Dnd41	blood
44	chr2:191397400-191398800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr2:191397400-191399000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:191397600-191398600	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr2:191397800-191398800	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr2:191397800-191399000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr2:191397800-191401000	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr2:191398000-191398400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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