Variant report

Variant	rs10489177
Chromosome Location	chr1:169762807-169762808
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169737043..169739732-chr1:169761259..169763805,3	MCF-7	breast:
2	chr1:169679878..169683283-chr1:169762041..169765464,5	MCF-7	breast:
3	chr1:169738855..169740454-chr1:169761742..169763292,2	K562	blood:
4	chr1:169680417..169682445-chr1:169762164..169765185,3	MCF-7	breast:
5	chr1:169454326..169457851-chr1:169761976..169765744,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117479	Chromatin interaction
ENSG00000213062	Chromatin interaction
ENSG00000188404	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10159425	0.84[ASN][1000 genomes]
rs10489170	1.00[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs10753796	0.93[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10753798	0.81[CHB][hapmap]
rs10800477	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800478	0.81[CHB][hapmap]
rs10800482	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10919243	0.87[CHB][hapmap]
rs10919260	1.00[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs10919270	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs10919271	0.85[CEU][hapmap]
rs10919272	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs11804170	0.85[CEU][hapmap]
rs12049325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12127655	0.82[MEX][hapmap]
rs12128754	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12135656	0.90[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.92[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12135826	0.92[EUR][1000 genomes]
rs12138675	1.00[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs12760433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2143121	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2272916	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3753311	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6427223	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427229	0.91[MEX][hapmap]
rs6658548	0.92[EUR][1000 genomes]
rs6670253	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6679646	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6688806	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7552710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9787237	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9803717	0.81[CHB][hapmap]
rs9803860	0.81[CHB][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	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10489177	CREG1	cis	cerebellum	SCAN
rs10489177	C1orf112	cis	cerebellum	SCAN
rs10489177	LMX1A	cis	parietal	SCAN
rs10489177	C1orf156	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169753600-169763000	Weak transcription	HMEC	breast
2	chr1:169757400-169763000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:169757400-169763000	Weak transcription	Thymus	Thymus
4	chr1:169757400-169763200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:169757600-169763000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr1:169758200-169763200	Weak transcription	Adipose Nuclei	Adipose
7	chr1:169758200-169763200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:169758600-169763000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:169758600-169763200	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:169758600-169763200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:169758600-169763400	Weak transcription	Gastric	stomach
12	chr1:169758800-169763000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:169758800-169763000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:169758800-169763200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:169758800-169763200	Weak transcription	HSMM	muscle
16	chr1:169758800-169763600	Weak transcription	Spleen	Spleen
17	chr1:169759000-169763000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:169759000-169763000	Weak transcription	A549	lung
19	chr1:169759200-169763000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:169759200-169763200	Weak transcription	Ovary	ovary
21	chr1:169759200-169763200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:169759400-169763000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:169759600-169763000	Weak transcription	Brain Substantia Nigra	brain
24	chr1:169759600-169763200	Weak transcription	Pancreas	Pancrea
25	chr1:169759800-169763200	Weak transcription	Fetal Intestine Large	intestine
26	chr1:169759800-169763200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:169760000-169763000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:169760200-169763000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:169760400-169763000	Weak transcription	Fetal Stomach	stomach
30	chr1:169760400-169763200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:169760400-169763200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:169760400-169763200	Weak transcription	Lung	lung
33	chr1:169760400-169763200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:169760400-169763200	Weak transcription	Psoas Muscle	Psoas
35	chr1:169760400-169763200	Weak transcription	NH-A	brain
36	chr1:169760400-169763200	Weak transcription	NHDF-Ad	bronchial
37	chr1:169760400-169763600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:169760600-169763000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:169760600-169763000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:169760600-169763000	Weak transcription	HUVEC	blood vessel
41	chr1:169760800-169763000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:169760800-169763200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:169760800-169763200	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr1:169761000-169763200	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr1:169761000-169763200	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr1:169761200-169763000	Weak transcription	Primary B cells from peripheral blood	blood
47	chr1:169761200-169763000	Weak transcription	NHLF	lung
48	chr1:169761400-169763000	Enhancers	Liver	Liver
49	chr1:169761400-169763000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr1:169761400-169763000	Weak transcription	Osteobl	bone

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