Variant report

Variant	rs1224488
Chromosome Location	chr6:36984718-36984719
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr6:36984711-36985152	HL-60	blood:	n/a	chr6:36984733-36984746 chr6:36984735-36984744

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36967024..36973771-chr6:36979699..36986633,7	K562	blood:
2	chr6:36885661..36888291-chr6:36984443..36986353,2	MCF-7	breast:
3	chr6:36851998..36854194-chr6:36984664..36987550,2	K562	blood:
4	chr6:36950593..36954224-chr6:36982678..36985968,4	K562	blood:
5	chr6:36853323..36855502-chr6:36984627..36986609,2	MCF-7	breast:
6	chr6:36984537..36986387-chr6:37185283..37186922,2	K562	blood:
7	chr6:36952434..36955977-chr6:36983476..36987276,5	MCF-7	breast:
8	chr6:36852005..36855458-chr6:36984429..36987560,3	K562	blood:
9	chr6:36951647..36954567-chr6:36984468..36987638,6	K562	blood:
10	chr6:36952577..36955767-chr6:36983861..36986521,4	MCF-7	breast:

No data

Variant related genes	Relation type
FGD2	TF binding region
ENSG00000172738	Chromatin interaction
ENSG00000137409	Chromatin interaction
ENSG00000146192	Chromatin interaction
ENSG00000198663	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12199978	1.00[YRI][hapmap]
rs1224487	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1224491	0.86[ASN][1000 genomes]
rs1228575	0.88[ASN][1000 genomes]
rs1547571	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1724094	0.86[ASN][1000 genomes]
rs1753301	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2025998	0.88[ASN][1000 genomes]
rs4317401	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4711482	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6457974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6457980	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6939869	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7750403	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7751821	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs831484	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs831487	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs831489	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs831491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs831497	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs831499	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs831500	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs831502	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs913499	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs913500	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9296207	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs9366927	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9380637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv518386	chr6:36942746-37037670	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv885816	chr6:36965099-36999682	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv515488	chr6:36978745-36989587	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1224488	FGD2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36974200-36987000	Weak transcription	Right Atrium	heart
2	chr6:36974800-36985000	Weak transcription	Brain Substantia Nigra	brain
3	chr6:36975000-36985800	Weak transcription	Fetal Intestine Small	intestine
4	chr6:36975400-36985400	Weak transcription	Right Ventricle	heart
5	chr6:36975400-36988600	Weak transcription	Gastric	stomach
6	chr6:36975600-36985800	Weak transcription	Stomach Mucosa	stomach
7	chr6:36975600-36988200	Weak transcription	Esophagus	oesophagus
8	chr6:36975600-36989600	Weak transcription	Thymus	Thymus
9	chr6:36976000-36985200	Weak transcription	Placenta	Placenta
10	chr6:36976000-36986200	Weak transcription	Colonic Mucosa	Colon
11	chr6:36976200-36984800	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:36976200-36985800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:36976200-36985800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:36977000-36985800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:36977000-36986200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr6:36977400-36984800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:36977400-36986200	Weak transcription	Adipose Nuclei	Adipose
18	chr6:36978000-36985600	Strong transcription	Primary B cells from cord blood	blood
19	chr6:36978800-36985400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr6:36979600-36985200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr6:36979800-36985400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr6:36980400-36985600	Strong transcription	GM12878-XiMat	blood
23	chr6:36981000-36985000	Weak transcription	Fetal Stomach	stomach
24	chr6:36982000-36985200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:36982200-36985600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:36983400-36995000	Weak transcription	Lung	lung
27	chr6:36983600-36985600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:36983800-36985600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr6:36984000-36985400	Weak transcription	Spleen	Spleen
30	chr6:36984600-36985800	Weak transcription	Osteobl	bone
31	chr6:36984600-36987200	Enhancers	Fetal Thymus	thymus

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