Variant report

Variant	rs4936580
Chromosome Location	chr11:121007777-121007778
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	STAT5A	chr11:121007670-121008062	GM12878	blood:	n/a	n/a
2	SUZ12	chr11:121007742-121008112	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr11:121007750-121007983	H1-hESC	embryonic stem cell:	n/a	n/a
4	NFATC1	chr11:121007626-121008172	GM12878	blood:	n/a	n/a
5	PBX3	chr11:121007712-121008046	GM12878	blood:	n/a	n/a
6	BCL3	chr11:121007643-121008110	GM12878	blood:	n/a	n/a
7	NFATC1	chr11:121007658-121008108	GM12878	blood:	n/a	n/a
8	BCL3	chr11:121007631-121008081	GM12878	blood:	n/a	n/a
9	TCF3	chr11:121007767-121008023	GM12878	blood:	n/a	n/a
10	TCF3	chr11:121007747-121008142	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
TECTA	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11218155	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11218160	0.83[YRI][hapmap]
rs12361100	0.89[ASN][1000 genomes]
rs12575628	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2155364	0.84[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2155365	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2155369	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs22298	0.90[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4427574	0.89[YRI][hapmap]
rs4554895	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs481703	0.85[JPT][hapmap]
rs492294	0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4935760	0.89[YRI][hapmap]
rs4936579	0.89[YRI][hapmap]
rs510722	0.82[EUR][1000 genomes]
rs543119	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs552580	0.81[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs559301	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs560365	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs560401	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs561195	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs561227	0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs562281	0.81[EUR][1000 genomes]
rs576271	0.80[EUR][1000 genomes]
rs582876	0.81[EUR][1000 genomes]
rs588917	0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs589790	0.96[ASN][1000 genomes]
rs592160	0.81[EUR][1000 genomes]
rs594951	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs596882	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs599894	1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs605379	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs618523	0.82[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs620896	0.81[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs633012	0.80[EUR][1000 genomes]
rs638463	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs638496	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs640332	0.81[EUR][1000 genomes]
rs662496	0.85[JPT][hapmap]
rs663319	0.82[YRI][hapmap]
rs663435	0.81[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs677336	0.81[EUR][1000 genomes]
rs677775	0.80[EUR][1000 genomes]
rs686882	0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs688641	0.85[JPT][hapmap];0.81[EUR][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	nsv524	chr11:120963503-121008167	Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3402556	chr11:121005842-121010040	Weak transcription Enhancers Strong transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4936580	HINFP	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120993200-121008000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr11:120994000-121016200	Weak transcription	Brain Substantia Nigra	brain
3	chr11:120994400-121042400	Weak transcription	Brain Hippocampus Middle	brain
4	chr11:120996800-121016400	Weak transcription	Ovary	ovary
5	chr11:120996800-121037800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr11:120998400-121007800	Weak transcription	Fetal Brain Male	brain
7	chr11:120998800-121007800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:120998800-121009400	Weak transcription	Spleen	Spleen
9	chr11:120999000-121007800	Weak transcription	Gastric	stomach
10	chr11:120999000-121011200	Weak transcription	Aorta	Aorta
11	chr11:120999200-121016200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr11:120999600-121007800	Weak transcription	Brain Germinal Matrix	brain
13	chr11:120999600-121041600	Weak transcription	Brain Anterior Caudate	brain
14	chr11:121000000-121025200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr11:121001000-121008400	Weak transcription	Fetal Brain Female	brain
16	chr11:121001200-121007800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:121001200-121012000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr11:121001400-121028000	Weak transcription	Fetal Stomach	stomach
19	chr11:121003200-121007800	Weak transcription	Pancreas	Pancrea
20	chr11:121005800-121023600	Weak transcription	Left Ventricle	heart
21	chr11:121006000-121024800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr11:121006400-121035400	Weak transcription	Brain Angular Gyrus	brain
23	chr11:121006400-121040200	Weak transcription	Right Ventricle	heart
24	chr11:121006600-121010000	Weak transcription	Fetal Heart	heart
25	chr11:121006600-121034800	Weak transcription	HSMMtube	muscle
26	chr11:121007000-121028800	Weak transcription	Fetal Muscle Leg	muscle
27	chr11:121007200-121011400	Strong transcription	Skeletal Muscle Male	skeletal muscle

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