Variant report

Variant	rs37966
Chromosome Location	chr7:8005868-8005869
allele	C/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	MTA3	chr7:8004980-8006734	GM12878	blood:	n/a	n/a
2	MEF2C	chr7:8005671-8006317	GM12878	blood:	n/a	chr7:8006009-8006024 chr7:8005852-8005866 chr7:8005850-8005871
3	CUX1	chr7:8005639-8006333	GM12878	blood:	n/a	chr7:8006167-8006176 chr7:8006168-8006182
4	RUNX3	chr7:8005066-8006379	GM12878	blood:	n/a	chr7:8005284-8005301
5	EP300	chr7:8004043-8006407	SK-N-SH	brain:	n/a	chr7:8006347-8006361 chr7:8004197-8004211 chr7:8004081-8004095 chr7:8005414-8005428
6	FOXM1	chr7:8005514-8006346	GM12878	blood:	n/a	n/a
7	CEBPB	chr7:8005322-8006375	GM12878	blood:	n/a	n/a
8	NFIC	chr7:8005105-8006471	GM12878	blood:	n/a	n/a
9	EP300	chr7:8005568-8006285	GM12878	blood:	n/a	n/a
10	STAT5A	chr7:8005794-8006207	GM12878	blood:	n/a	n/a
11	EP300	chr7:8005571-8006084	GM12878	blood:	n/a	n/a
12	NFATC1	chr7:8005746-8006299	GM12878	blood:	n/a	n/a
13	ATF2	chr7:8005483-8006361	GM12878	blood:	n/a	n/a
14	MEF2A	chr7:8005513-8006407	GM12878	blood:	n/a	chr7:8005852-8005866 chr7:8005564-8005579 chr7:8005850-8005871
15	MEF2A	chr7:8005702-8006260	GM12878	blood:	n/a	chr7:8005852-8005866 chr7:8005850-8005871
16	BCL11A	chr7:8005776-8006233	GM12878	blood:	n/a	n/a
17	NFATC1	chr7:8005663-8006220	GM12878	blood:	n/a	n/a
18	BATF	chr7:8005794-8006183	GM12878	blood:	n/a	n/a
19	BCL3	chr7:8005771-8006239	GM12878	blood:	n/a	n/a
20	FOXM1	chr7:8005532-8006265	GM12878	blood:	n/a	n/a
21	ZNF384	chr7:8005864-8006698	GM12878	blood:	n/a	chr7:8006683-8006691
22	NFIC	chr7:8005557-8006514	GM12878	blood:	n/a	n/a
23	BHLHE40	chr7:8005844-8006172	GM12878	blood:	n/a	n/a
24	ATF2	chr7:8005429-8006500	GM12878	blood:	n/a	n/a
25	PML	chr7:8005405-8006356	GM12878	blood:	n/a	n/a
26	RUNX3	chr7:8005489-8006264	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:7719627..7722096-chr7:8004642..8007515,2	MCF-7	breast:

Variant related genes	Relation type
GLCCI1	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10241457	0.83[GIH][hapmap];0.84[TSI][hapmap]
rs37962	0.97[EUR][1000 genomes]
rs37963	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs37964	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs37965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs37967	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs37970	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs37977	0.83[GIH][hapmap];0.86[TSI][hapmap]
rs37981	0.87[TSI][hapmap]
rs37995	0.80[GIH][hapmap];0.82[TSI][hapmap]
rs37998	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs38012	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs38013	0.86[GIH][hapmap];0.84[TSI][hapmap]
rs38018	0.81[GIH][hapmap];0.87[TSI][hapmap]
rs4720761	0.83[GIH][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1030180	chr7:7860424-8059221	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv3346837	chr7:7915187-8068557	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1020161	chr7:7929384-8047553	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs37966	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7985400-8007600	Weak transcription	Psoas Muscle	Psoas
2	chr7:7986800-8007800	Weak transcription	Ovary	ovary
3	chr7:7996800-8007400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:8002600-8007800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:8003000-8007200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:8003000-8007200	Weak transcription	NHDF-Ad	bronchial
7	chr7:8003000-8007400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr7:8003200-8007000	Weak transcription	Osteobl	bone
9	chr7:8003200-8007200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:8003200-8007600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:8003200-8007600	Weak transcription	NH-A	brain
12	chr7:8003800-8006000	Enhancers	Primary T cells from cord blood	blood
13	chr7:8003800-8007600	Enhancers	Fetal Thymus	thymus
14	chr7:8004400-8006000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr7:8004600-8007000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr7:8004800-8007000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:8005000-8007000	Enhancers	Thymus	Thymus
18	chr7:8005000-8007200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr7:8005200-8006000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr7:8005200-8006200	Flanking Active TSS	GM12878-XiMat	blood
21	chr7:8005200-8007000	Weak transcription	Dnd41	blood
22	chr7:8005400-8006400	Weak transcription	Primary B cells from cord blood	blood
23	chr7:8005400-8006400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr7:8005400-8007000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr7:8005400-8007200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:8005600-8006600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr7:8005600-8007000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr7:8005600-8007000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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