Variant report

Variant	rs41417950
Chromosome Location	chr2:12195782-12195783
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:12194778..12196811-chr2:12221641..12223390,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11675258	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675302	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11695831	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11695912	1.00[YRI][hapmap]
rs12998142	1.00[YRI][hapmap]
rs34344432	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55824035	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56139916	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58281155	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744880	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72777651	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv999704	chr2:12153766-12243960	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1005069	chr2:12161023-12242734	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1000696	chr2:12162843-12241022	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41417950	GREB1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:12188800-12196000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:12189000-12196000	Weak transcription	Spleen	Spleen
3	chr2:12189000-12197200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:12189400-12197000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr2:12192400-12196400	Weak transcription	HSMM	muscle
6	chr2:12192400-12197000	Weak transcription	HSMMtube	muscle
7	chr2:12192400-12198800	Weak transcription	NHLF	lung
8	chr2:12192600-12197200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:12192600-12197400	Weak transcription	Osteobl	bone
10	chr2:12192600-12199000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:12193200-12196600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:12193200-12198800	Weak transcription	NHDF-Ad	bronchial
13	chr2:12193400-12197000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:12194600-12200200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:12194800-12196000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:12195000-12196200	Enhancers	Brain Germinal Matrix	brain
17	chr2:12195000-12197200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:12195000-12197800	Enhancers	Fetal Muscle Leg	muscle
19	chr2:12195000-12200800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:12195200-12200600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr2:12195400-12197400	Weak transcription	Fetal Stomach	stomach
22	chr2:12195400-12200600	Enhancers	Primary B cells from peripheral blood	blood
23	chr2:12195600-12197400	Enhancers	Dnd41	blood
24	chr2:12195600-12200600	Enhancers	Primary hematopoietic stem cells	blood

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