Variant report

Variant	rs3199966
Chromosome Location	chr9:108147763-108147764
allele	G/T
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	POLR2A	chr9:108147544-108148291	PBDE	blood:	n/a	n/a
2	RUNX3	chr9:108147545-108148058	GM12878	blood:	n/a	n/a
3	SMC3	chr9:108147678-108148007	GM12878	blood:	n/a	n/a
4	STAT3	chr9:108147751-108147850	MCF10A-Er-Src	breast:	n/a	chr9:108147824-108147835
5	IRF1	chr9:108147688-108147996	K562	blood:	n/a	chr9:108147825-108147839 chr9:108147825-108147835 chr9:108147819-108147829 chr9:108147823-108147837 chr9:108147819-108147833 chr9:108147821-108147835 chr9:108147817-108147837 chr9:108147819-108147840 chr9:108147823-108147834 chr9:108147817-108147831 chr9:108147818-108147831 chr9:108147818-108147831 chr9:108147827-108147836
6	IKZF1	chr9:108147615-108148213	GM12878	blood:	n/a	n/a
7	IRF1	chr9:108147651-108148035	K562	blood:	n/a	chr9:108147825-108147839 chr9:108147825-108147835 chr9:108147819-108147829 chr9:108147823-108147837 chr9:108147819-108147833 chr9:108147821-108147835 chr9:108147817-108147837 chr9:108147819-108147840 chr9:108147823-108147834 chr9:108147817-108147831 chr9:108147818-108147831 chr9:108147818-108147831 chr9:108147827-108147836
8	SPI1	chr9:108147321-108148458	GM12878	blood:	n/a	chr9:108147829-108147842 chr9:108147826-108147835 chr9:108147831-108147838 chr9:108147828-108147841
9	BCLAF1	chr9:108147599-108148087	GM12878	blood:	n/a	chr9:108147820-108147829 chr9:108148016-108148029 chr9:108147826-108147835
10	NFIC	chr9:108147529-108148192	GM12878	blood:	n/a	n/a
11	SPI1	chr9:108147646-108148069	HL-60	blood:	n/a	chr9:108147829-108147842 chr9:108147826-108147835 chr9:108147831-108147838 chr9:108147828-108147841
12	EGR1	chr9:108147708-108147863	GM12878	blood:	n/a	chr9:108147829-108147838 chr9:108147794-108147808
13	RCOR1	chr9:108147710-108148011	GM12878	blood:	n/a	n/a
14	ATF2	chr9:108147505-108148055	GM12878	blood:	n/a	n/a
15	TEAD4	chr9:108147650-108148103	K562	blood:	n/a	n/a
16	MYC	chr9:108147742-108147944	K562	blood:	n/a	n/a
17	EBF1	chr9:108147731-108148095	GM12878	blood:	n/a	n/a
18	IRF4	chr9:108147553-108148078	GM12878	blood:	n/a	chr9:108147819-108147840
19	SPI1	chr9:108147573-108148074	GM12878	blood:	n/a	chr9:108147829-108147842 chr9:108147826-108147835 chr9:108147831-108147838 chr9:108147828-108147841
20	SPI1	chr9:108147688-108147968	K562	blood:	n/a	chr9:108147829-108147842 chr9:108147826-108147835 chr9:108147831-108147838 chr9:108147828-108147841
21	POLR2A	chr9:108147753-108148015	GM12891	blood:	n/a	n/a
22	POLR2A	chr9:108147522-108148110	U87	brain:	n/a	n/a
23	ATF1	chr9:108147725-108148027	K562	blood:	n/a	n/a
24	RCOR1	chr9:108147640-108148324	K562	blood:	n/a	n/a
25	POLR2A	chr9:108147700-108148058	U87	brain:	n/a	n/a
26	EP300	chr9:108147674-108148110	GM12878	blood:	n/a	chr9:108147820-108147834 chr9:108147826-108147840
27	MYC	chr9:108147685-108147994	K562	blood:	n/a	n/a
28	RUNX3	chr9:108147613-108147954	GM12878	blood:	n/a	n/a
29	POLR2A	chr9:108147647-108148139	GM12892	blood:	n/a	n/a
30	SPI1	chr9:108147568-108148134	GM12891	blood:	n/a	chr9:108147829-108147842 chr9:108147826-108147835 chr9:108147831-108147838 chr9:108147828-108147841
31	SPI1	chr9:108147651-108148001	GM12878	blood:	n/a	chr9:108147829-108147842 chr9:108147826-108147835 chr9:108147831-108147838 chr9:108147828-108147841
32	GATA1	chr9:108147582-108148329	PBDE	blood:	n/a	chr9:108147882-108147891 chr9:108147883-108147900 chr9:108147828-108147838
33	POLR2A	chr9:108147717-108148083	Gliobla	brain:	n/a	n/a
34	TAL1	chr9:108147742-108148046	K562	blood:	n/a	chr9:108147882-108147900
35	IRF1	chr9:108146940-108148188	K562	blood:	n/a	chr9:108147825-108147839 chr9:108147825-108147835 chr9:108147819-108147829 chr9:108147823-108147837 chr9:108148076-108148089 chr9:108147819-108147833 chr9:108147821-108147835 chr9:108147817-108147837 chr9:108147819-108147840 chr9:108147823-108147834 chr9:108147817-108147831 chr9:108147818-108147831 chr9:108148146-108148157 chr9:108147818-108147831 chr9:108147827-108147836
36	WRNIP1	chr9:108147670-108148154	GM12878	blood:	n/a	n/a
37	MTA3	chr9:108147538-108148260	GM12878	blood:	n/a	n/a
38	SPI1	chr9:108147581-108148105	HL-60	blood:	n/a	chr9:108147829-108147842 chr9:108147826-108147835 chr9:108147831-108147838 chr9:108147828-108147841
39	TBL1XR1	chr9:108147610-108148178	K562	blood:	n/a	n/a
40	POLR2A	chr9:108147583-108148110	U87	brain:	n/a	n/a
41	JUND	chr9:108147724-108148031	K562	blood:	n/a	n/a
42	GATA3	chr9:108147608-108148008	T-47D	breast:	n/a	chr9:108147882-108147891 chr9:108147883-108147900 chr9:108147828-108147838
43	REST	chr9:108147647-108147991	Hela-S3	cervix:	n/a	n/a
44	HCFC1	chr9:108147758-108147977	K562	blood:	n/a	n/a
45	RCOR1	chr9:108147717-108148034	K562	blood:	n/a	n/a
46	SPI1	chr9:108147630-108148127	GM12891	blood:	n/a	chr9:108147829-108147842 chr9:108147826-108147835 chr9:108147831-108147838 chr9:108147828-108147841

Variant related genes	Relation type
SLC44A1	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10123494	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10491810	1.00[ASN][1000 genomes]
rs10820801	0.85[GIH][hapmap];0.84[AMR][1000 genomes]
rs10991629	0.86[MEX][hapmap]
rs10991639	0.94[ASW][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12339823	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340765	1.00[ASN][1000 genomes]
rs12342542	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344130	0.80[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13294525	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13294539	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1410837	1.00[ASN][1000 genomes]
rs1410839	1.00[ASW][hapmap];0.85[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1553870	1.00[ASN][1000 genomes]
rs1553873	1.00[ASN][1000 genomes]
rs16924529	0.80[CEU][hapmap];1.00[ASN][1000 genomes]
rs16924530	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17246524	1.00[ASN][1000 genomes]
rs17305886	1.00[ASN][1000 genomes]
rs17305963	1.00[ASN][1000 genomes]
rs2417615	0.81[AMR][1000 genomes]
rs2771031	1.00[ASN][1000 genomes]
rs2771033	0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2771040	1.00[ASW][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2812314	1.00[ASN][1000 genomes]
rs2812316	1.00[ASN][1000 genomes]
rs34750132	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35603631	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41296093	1.00[ASN][1000 genomes]
rs4549843	0.85[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs6479311	0.80[GIH][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6479313	0.80[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs6479314	0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6479316	0.84[AMR][1000 genomes]
rs7024985	1.00[ASW][hapmap];0.80[LWK][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7029443	0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs7045091	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs724069	1.00[ASN][1000 genomes]
rs7858401	0.80[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs7865985	0.85[MEX][hapmap]
rs907230	0.86[MEX][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3199966	CYLC2	cis	parietal	SCAN
rs3199966	SLC44A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108055600-108151200	Weak transcription	Esophagus	oesophagus
2	chr9:108091600-108150400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:108092000-108148000	Weak transcription	Psoas Muscle	Psoas
4	chr9:108093200-108149800	Weak transcription	HUVEC	blood vessel
5	chr9:108096200-108164200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:108100200-108149600	Weak transcription	Pancreas	Pancrea
7	chr9:108105000-108149600	Weak transcription	Right Ventricle	heart
8	chr9:108105000-108151200	Weak transcription	Gastric	stomach
9	chr9:108105000-108154800	Weak transcription	Small Intestine	intestine
10	chr9:108105200-108149800	Weak transcription	NHDF-Ad	bronchial
11	chr9:108121600-108157000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:108121800-108148600	Weak transcription	A549	lung
13	chr9:108122400-108148200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr9:108122600-108153400	Weak transcription	Stomach Mucosa	stomach
15	chr9:108123600-108154400	Weak transcription	Colonic Mucosa	Colon
16	chr9:108124400-108151000	Weak transcription	Fetal Brain Male	brain
17	chr9:108124600-108151800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:108125000-108166800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr9:108125400-108149800	Weak transcription	HSMMtube	muscle
20	chr9:108125600-108157000	Weak transcription	Osteobl	bone
21	chr9:108126000-108152000	Weak transcription	Brain Germinal Matrix	brain
22	chr9:108126400-108147800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr9:108127000-108147800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr9:108127200-108151800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr9:108128200-108151400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr9:108130200-108147800	Weak transcription	Ovary	ovary
27	chr9:108136200-108152000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:108137400-108150600	Weak transcription	Fetal Heart	heart
29	chr9:108137800-108147800	Weak transcription	Fetal Muscle Leg	muscle
30	chr9:108137800-108155400	Weak transcription	Lung	lung
31	chr9:108137800-108156200	Weak transcription	Fetal Stomach	stomach
32	chr9:108137800-108156400	Weak transcription	Aorta	Aorta
33	chr9:108137800-108157200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:108137800-108158200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:108138000-108147800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr9:108138000-108156400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:108138000-108156400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:108138400-108147800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:108138400-108149600	Weak transcription	Placenta	Placenta
40	chr9:108138600-108153000	Weak transcription	Fetal Brain Female	brain
41	chr9:108138800-108152000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr9:108142200-108151400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:108143600-108157000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr9:108144400-108148800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:108145200-108148400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:108145200-108148400	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr9:108145200-108148600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr9:108145400-108147800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr9:108145400-108148800	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr9:108145400-108149000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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