Variant report

Variant	rs12199978
Chromosome Location	chr6:36983192-36983193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:36967024..36973771-chr6:36979699..36986633,7	K562	blood:
2	chr6:36950593..36954224-chr6:36982678..36985968,4	K562	blood:

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction
ENSG00000146192	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10947659	1.00[JPT][hapmap]
rs12210148	1.00[JPT][hapmap]
rs1224488	1.00[YRI][hapmap]
rs16889362	1.00[JPT][hapmap]
rs16889370	1.00[JPT][hapmap]
rs2395668	1.00[JPT][hapmap]
rs7757939	1.00[JPT][hapmap]
rs9462264	1.00[JPT][hapmap]
rs9470493	1.00[JPT][hapmap]

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
rs12199978	FGD2	cis	multi-tissue	Pritchard

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36974200-36987000	Weak transcription	Right Atrium	heart
2	chr6:36974800-36984600	Weak transcription	Fetal Thymus	thymus
3	chr6:36974800-36985000	Weak transcription	Brain Substantia Nigra	brain
4	chr6:36975000-36985800	Weak transcription	Fetal Intestine Small	intestine
5	chr6:36975400-36985400	Weak transcription	Right Ventricle	heart
6	chr6:36975400-36988600	Weak transcription	Gastric	stomach
7	chr6:36975600-36985800	Weak transcription	Stomach Mucosa	stomach
8	chr6:36975600-36988200	Weak transcription	Esophagus	oesophagus
9	chr6:36975600-36989600	Weak transcription	Thymus	Thymus
10	chr6:36976000-36985200	Weak transcription	Placenta	Placenta
11	chr6:36976000-36986200	Weak transcription	Colonic Mucosa	Colon
12	chr6:36976200-36983200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr6:36976200-36984800	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:36976200-36985800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:36976200-36985800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:36977000-36985800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:36977000-36986200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr6:36977400-36984800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:36977400-36986200	Weak transcription	Adipose Nuclei	Adipose
20	chr6:36977800-36984000	Strong transcription	Spleen	Spleen
21	chr6:36978000-36985600	Strong transcription	Primary B cells from cord blood	blood
22	chr6:36978800-36985400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr6:36979600-36985200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr6:36979800-36985400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr6:36980400-36985600	Strong transcription	GM12878-XiMat	blood
26	chr6:36980800-36983400	Strong transcription	Lung	lung
27	chr6:36981000-36985000	Weak transcription	Fetal Stomach	stomach
28	chr6:36982000-36985200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:36982200-36985600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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