Variant report

Variant	rs514163
Chromosome Location	chr1:165885147-165885148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:165737165..165740400-chr1:165883348..165886412,3	MCF-7	breast:
2	chr1:165569014..165571063-chr1:165883495..165885234,2	K562	blood:
3	chr1:165570598..165571161-chr1:165885123..165885647,2	K562	blood:
4	chr1:165567537..165571496-chr1:165881949..165885234,3	K562	blood:

Variant related genes	Relation type
ENSG00000236206	Chromatin interaction
ENSG00000224358	Chromatin interaction
ENSG00000143183	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12118019	0.99[EUR][1000 genomes]
rs12119028	0.99[EUR][1000 genomes]
rs12569109	0.98[EUR][1000 genomes]
rs1663841	0.92[EUR][1000 genomes]
rs16851987	1.00[JPT][hapmap]
rs1768900	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3790654	0.91[CEU][hapmap];0.91[GIH][hapmap]
rs3790668	0.95[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs3790669	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790670	0.92[EUR][1000 genomes]
rs3790674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656467	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4657489	0.82[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs474766	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs475558	0.99[EUR][1000 genomes]
rs504436	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs505877	0.99[ASN][1000 genomes]
rs530717	0.99[EUR][1000 genomes]
rs533929	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs537068	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs561315	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs576213	0.99[EUR][1000 genomes]
rs6426943	0.99[EUR][1000 genomes]
rs6682285	0.86[CEU][hapmap];0.95[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs9787031	0.99[EUR][1000 genomes]

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	nsv872509	chr1:165885147-165917109	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs514163	ITLN2	cis	cerebellum	SCAN
rs514163	SLAMF1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165858600-165902400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:165879200-165886200	Enhancers	Stomach Mucosa	stomach
3	chr1:165879400-165894600	Weak transcription	Aorta	Aorta
4	chr1:165880000-165885200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:165880000-165888400	Weak transcription	Spleen	Spleen
6	chr1:165880600-165889000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:165880600-165894200	Weak transcription	Right Atrium	heart
8	chr1:165880800-165902600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:165881000-165886800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:165881000-165887200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:165881200-165885200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:165881200-165885200	Enhancers	HepG2	liver
13	chr1:165881800-165888400	Weak transcription	Fetal Intestine Small	intestine
14	chr1:165882200-165885200	Weak transcription	Esophagus	oesophagus
15	chr1:165882200-165889200	Weak transcription	Fetal Brain Female	brain
16	chr1:165882200-165889400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:165882200-165894200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:165883200-165885200	Enhancers	HSMM	muscle
19	chr1:165883600-165888400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:165883600-165896400	Weak transcription	Dnd41	blood
21	chr1:165884200-165885400	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:165884200-165885800	Enhancers	HSMMtube	muscle
23	chr1:165884400-165885400	Enhancers	Pancreas	Pancrea
24	chr1:165884600-165885200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:165884600-165885200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:165884600-165885200	Enhancers	Fetal Muscle Leg	muscle
27	chr1:165884600-165885400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:165884600-165885400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:165884600-165885400	Enhancers	HMEC	breast
30	chr1:165884600-165885600	Enhancers	Duodenum Mucosa	Duodenum
31	chr1:165884800-165885400	Enhancers	Hela-S3	cervix
32	chr1:165885000-165885200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:165885000-165885400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:165885000-165885400	Enhancers	Gastric	stomach
35	chr1:165885000-165885400	Enhancers	Small Intestine	intestine
36	chr1:165885000-165885800	Enhancers	Fetal Heart	heart

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