Variant report

Variant	rs870117
Chromosome Location	chr1:214505752-214505753
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:214387385..214388192-chr1:214504873..214505786,3	MCF-7	breast:
2	chr1:214391165..214391781-chr1:214505289..214505984,2	MCF-7	breast:
3	chr1:214452237..214456498-chr1:214498464..214506870,12	MCF-7	breast:
4	chr1:214505285..214508273-chr1:214509081..214512875,3	K562	blood:
5	chr1:214434555..214435680-chr1:214504881..214505799,6	K562	blood:
6	chr1:214505230..214508273-chr1:214509081..214512875,4	K562	blood:
7	chr1:214505527..214506582-chr1:214801187..214801906,3	MCF-7	breast:
8	chr1:214504942..214505826-chr1:214758292..214758918,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143499	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10864093	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10864094	0.87[ASN][1000 genomes]
rs11120289	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12081918	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12081925	0.95[ASN][1000 genomes]
rs12095774	0.93[ASN][1000 genomes]
rs12725392	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12737638	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1874804	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088512	0.95[ASN][1000 genomes]
rs34932055	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754136	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767843	0.86[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6676709	0.87[ASW][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs6704032	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs870117	GALC	trans	parietal	SCAN
rs870117	SMYD2	Cis_1M	lymphoblastoid	RTeQTL
rs870117	SMYD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214471000-214517400	Weak transcription	Fetal Kidney	kidney
2	chr1:214477400-214506400	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:214477400-214506400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:214477400-214511000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:214482200-214510600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:214484400-214510800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:214484800-214507800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:214484800-214522000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:214485000-214506400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:214485000-214513200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:214486200-214526000	Weak transcription	Psoas Muscle	Psoas
12	chr1:214487400-214509400	Strong transcription	Primary T cells from cord blood	blood
13	chr1:214487600-214506200	Weak transcription	Small Intestine	intestine
14	chr1:214487800-214510600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:214488200-214517600	Weak transcription	Brain Germinal Matrix	brain
16	chr1:214488200-214520800	Weak transcription	Hela-S3	cervix
17	chr1:214488800-214510600	Weak transcription	Fetal Brain Male	brain
18	chr1:214489400-214506200	Weak transcription	A549	lung
19	chr1:214489400-214506600	Weak transcription	Ovary	ovary
20	chr1:214490800-214518200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:214491600-214506000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:214492800-214509200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:214493000-214510600	Weak transcription	Aorta	Aorta
24	chr1:214493000-214519800	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:214493000-214534600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:214493400-214508600	Strong transcription	HepG2	liver
27	chr1:214493800-214519000	Weak transcription	Fetal Thymus	thymus
28	chr1:214495400-214507400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr1:214495600-214510400	Weak transcription	NH-A	brain
30	chr1:214497800-214509000	Strong transcription	Dnd41	blood
31	chr1:214499600-214506200	Strong transcription	Fetal Stomach	stomach
32	chr1:214499800-214506200	Strong transcription	Fetal Intestine Large	intestine
33	chr1:214500000-214508800	Strong transcription	Fetal Intestine Small	intestine
34	chr1:214500200-214507200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr1:214500200-214510000	Weak transcription	GM12878-XiMat	blood
36	chr1:214501000-214506000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:214501800-214512000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:214501800-214517800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:214502000-214506800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:214502200-214506400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:214502200-214506600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr1:214502600-214510800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:214502600-214515000	Weak transcription	Brain Angular Gyrus	brain
44	chr1:214502800-214506200	Strong transcription	Fetal Muscle Leg	muscle
45	chr1:214502800-214506400	Weak transcription	HSMM	muscle
46	chr1:214502800-214506600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:214502800-214506600	Weak transcription	Osteobl	bone
48	chr1:214502800-214510400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:214503000-214506000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:214503000-214506200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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