Variant report

Variant	rs829955
Chromosome Location	chr2:169662024-169662025
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	chr2:169660149..169662783-chr2:169666363..169668736,2	MCF-7	breast:
2	chr2:169659017..169660754-chr2:169661000..169663704,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163072	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17265731	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17265949	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2010230	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2433679	0.89[ASN][1000 genomes]
rs2461362	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2461390	0.89[ASN][1000 genomes]
rs494120	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs498488	0.89[ASN][1000 genomes]
rs511013	1.00[CHB][hapmap]
rs551037	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs572411	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6433093	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs829960	0.89[ASN][1000 genomes]
rs830025	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs830026	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9287903	0.82[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915920	chr2:168851960-169696591	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs829955	KLHL23	cis	cerebellum	SCAN
rs829955	COBLL1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169656000-169666800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:169658600-169662200	Active TSS	Right Atrium	heart
3	chr2:169659000-169665800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:169659000-169668200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:169659200-169662200	Weak transcription	Spleen	Spleen
6	chr2:169659200-169666000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:169659200-169666600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:169659800-169662800	Active TSS	Adipose Nuclei	Adipose
9	chr2:169659800-169666600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:169659800-169672400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:169660000-169666600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:169660000-169676000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:169660000-169688200	Weak transcription	Placenta	Placenta
14	chr2:169660400-169662200	Flanking Active TSS	K562	blood
15	chr2:169660400-169662400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:169660600-169664800	Weak transcription	Small Intestine	intestine
17	chr2:169661000-169662200	Weak transcription	Psoas Muscle	Psoas
18	chr2:169661000-169666800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:169661000-169668200	Weak transcription	Ovary	ovary
20	chr2:169661200-169662200	Weak transcription	Left Ventricle	heart
21	chr2:169661200-169662200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:169661200-169662200	Enhancers	Stomach Mucosa	stomach
23	chr2:169661200-169664000	Enhancers	Fetal Heart	heart
24	chr2:169661200-169668600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:169661400-169676800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:169661800-169665600	Weak transcription	Fetal Intestine Large	intestine
27	chr2:169662000-169662200	Active TSS	Lung	lung
28	chr2:169662000-169662400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:169662000-169662400	Enhancers	Fetal Muscle Leg	muscle
30	chr2:169662000-169662600	Genic enhancers	Fetal Intestine Small	intestine
31	chr2:169662000-169662600	Genic enhancers	Gastric	stomach
32	chr2:169662000-169662800	Enhancers	Pancreas	Pancrea
33	chr2:169662000-169662800	Enhancers	Right Ventricle	heart
34	chr2:169662000-169670000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

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