Variant report

Variant	rs2298929
Chromosome Location	chr1:209822979-209822980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:209822794..209824585-chr1:209831466..209834009,2	K562	blood:
2	chr1:209810488..209814194-chr1:209821440..209824229,3	K562	blood:
3	chr1:209820434..209823363-chr1:209947209..209948890,2	K562	blood:
4	chr1:209822747..209824605-chr1:209978832..209981504,2	MCF-7	breast:
5	chr1:209809942..209814194-chr1:209821440..209824587,3	K562	blood:
6	chr1:209821933..209824497-chr1:209825601..209827307,2	MCF-7	breast:
7	chr1:209814818..209817682-chr1:209819640..209823452,3	MCF-7	breast:
8	chr1:209821625..209823154-chr1:209825610..209828128,2	MCF-7	breast:
9	chr1:209813134..209815855-chr1:209819487..209823509,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000117595	Chromatin interaction
ENSG00000196878	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10779510	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10863778	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12089972	0.99[ASN][1000 genomes]
rs2298924	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298927	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36051870	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	esv2762140	chr1:209816331-209830347	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2298929	SPATC1	trans	cerebellum	SCAN
rs2298929	RD3	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209814200-209825000	Enhancers	Fetal Muscle Leg	muscle
2	chr1:209814400-209823200	Genic enhancers	Fetal Intestine Large	intestine
3	chr1:209814600-209823200	Enhancers	Fetal Heart	heart
4	chr1:209814600-209826800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:209816000-209824200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
6	chr1:209817000-209825400	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr1:209817400-209824600	Weak transcription	Aorta	Aorta
8	chr1:209817600-209824800	Transcr. at gene 5' and 3'	HMEC	breast
9	chr1:209817800-209825800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:209817800-209826000	Weak transcription	Brain Angular Gyrus	brain
11	chr1:209818000-209826000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:209818200-209825800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:209818200-209826000	Weak transcription	Brain Substantia Nigra	brain
14	chr1:209818600-209825200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:209819000-209823000	Enhancers	Ovary	ovary
16	chr1:209819000-209823600	Enhancers	Right Atrium	heart
17	chr1:209819000-209825200	Enhancers	HSMM	muscle
18	chr1:209819200-209823000	Enhancers	Stomach Mucosa	stomach
19	chr1:209819200-209823200	Enhancers	Fetal Kidney	kidney
20	chr1:209819200-209824800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:209819200-209825000	Transcr. at gene 5' and 3'	NHEK	skin
22	chr1:209819200-209825400	Enhancers	NHLF	lung
23	chr1:209819200-209827400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:209819200-209831200	Enhancers	Pancreas	Pancrea
25	chr1:209819400-209823000	Enhancers	Psoas Muscle	Psoas
26	chr1:209819400-209823600	Enhancers	Left Ventricle	heart
27	chr1:209819400-209824000	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr1:209819800-209823200	Enhancers	Brain Germinal Matrix	brain
29	chr1:209819800-209824200	Weak transcription	Brain Anterior Caudate	brain
30	chr1:209819800-209825000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:209819800-209825000	Enhancers	NHDF-Ad	bronchial
32	chr1:209820000-209825400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:209820000-209825400	Enhancers	Stomach Smooth Muscle	stomach
34	chr1:209820000-209825600	Weak transcription	Fetal Brain Female	brain
35	chr1:209820000-209825800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:209820200-209823200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr1:209820400-209824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr1:209820400-209824400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:209820400-209826200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:209820800-209823200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:209820800-209824200	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:209820800-209825800	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr1:209820800-209826000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr1:209821000-209823200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:209821000-209826200	Weak transcription	Fetal Brain Male	brain
46	chr1:209821400-209824000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:209821600-209823200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:209821600-209823800	Enhancers	Placenta Amnion	Placenta Amnion
49	chr1:209821600-209824200	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr1:209821600-209825000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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