Variant report

Variant	rs12633488
Chromosome Location	chr3:105082543-105082544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:105082495-105082545	NHBE	bronchial:	n/a
2	chr3:105082495-105082545	Caco-2	colon:	n/a
3	chr3:105082495-105082545	AG09319	gingival:	n/a
4	chr3:105082495-105082545	HCT-116	colon:	n/a
5	chr3:105082495-105082545	K562	blood:	n/a
6	chr3:105082495-105082545	HCPEpiC	choroid plexus:	n/a
7	chr3:105082495-105082545	PrEC	prostate:	n/a
8	chr3:105082495-105082545	AG09309	skin:	n/a
9	chr3:105082495-105082545	NHDF-neo	bronchial:	n/a
10	chr3:105082495-105082545	NB4	blood:	n/a
11	chr3:105082495-105082545	BE2_C	brain:	n/a
12	chr3:105082495-105082545	HL-60	blood:	n/a
13	chr3:105082495-105082545	A549	lung:	n/a
14	chr3:105082495-105082545	MCF10A-Er-Src	breast:	n/a
15	chr3:105082495-105082545	HEEpiC	esophagus:	n/a
16	chr3:105082495-105082545	GM12891	blood:	n/a
17	chr3:105082495-105082545	AG04449	skin:	fetal
18	chr3:105082495-105082545	SK-N-MC	brain:	n/a
19	chr3:105082495-105082545	GM12892	blood:	n/a
20	chr3:105082495-105082545	ECC-1	luminal epithelium:	n/a
21	chr3:105082495-105082545	Jurkat	blood:	n/a
22	chr3:105082495-105082545	CMK	blood:	n/a
23	chr3:105082495-105082545	HepG2	liver:	n/a
24	chr3:105082495-105082545	BJ	skin:	n/a
25	chr3:105082495-105082545	HCF	heart:	n/a
26	chr3:105082495-105082545	HRPEpiC	eye:	n/a
27	chr3:105082495-105082545	SKMC	muscle:	n/a
28	chr3:105082495-105082545	HRCEpiC	kidney:	n/a
29	chr3:105082495-105082545	GM12878	blood:	n/a
30	chr3:105082495-105082545	ProgFib	skin:	n/a
31	chr3:105082495-105082545	SAEC	small airway:	n/a
32	chr3:105082495-105082545	PANC-1	pancreas:	n/a
33	chr3:105082495-105082545	LNCaP	prostate:	n/a
34	chr3:105082495-105082545	IMR90	lung:	fetal
35	chr3:105082495-105082545	HIPEpiC	eye:	n/a
36	chr3:105082495-105082545	Hepatocyte	liver:	n/a
37	chr3:105082495-105082545	H1-hESC	embryonic stem cell:	embryo
38	chr3:105082495-105082545	HCM	heart:	n/a
39	chr3:105082495-105082545	SK-N-SH_RA	brain:	n/a
40	chr3:105082495-105082545	PFSK-1	brain:	n/a
41	chr3:105082495-105082545	GM06990	blood:	n/a
42	chr3:105082495-105082545	HMEC	breast:	n/a
43	chr3:105082495-105082545	RPTEC	kidney:	n/a
44	chr3:105082495-105082545	NT2-D1	testis:	n/a
45	chr3:105082495-105082545	HRE	kidney:	n/a
46	chr3:105082495-105082545	MCF-7	breast:	n/a
47	chr3:105082495-105082545	AG10803	skin:	n/a
48	chr3:105082495-105082545	HEK293	kidney:	embryo
49	chr3:105082495-105082545	AoSMC	blood vessel:	n/a
50	chr3:105082495-105082545	AG04450	lung:	fetal

No data

Variant related genes	Relation type
ALCAM	CpG island

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1020110	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10433369	0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10446292	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10511244	0.88[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12186012	0.85[EUR][1000 genomes]
rs12186024	0.85[EUR][1000 genomes]
rs12491519	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12495149	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12630634	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637538	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1347792	0.88[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1347793	0.82[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs1438540	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16844719	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16844723	0.81[ASN][1000 genomes]
rs16851091	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851172	0.88[CHB][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs16851188	0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2007681	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2007688	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2164954	0.82[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5012306	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55639861	0.83[ASN][1000 genomes]
rs56052407	0.83[ASN][1000 genomes]
rs60073537	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6437591	0.88[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs6437592	0.83[ASN][1000 genomes]
rs6437593	0.83[ASN][1000 genomes]
rs6437594	0.83[ASN][1000 genomes]
rs73177460	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73177480	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73181308	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73183107	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73183124	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73185128	0.83[ASN][1000 genomes]
rs73185129	0.83[ASN][1000 genomes]
rs73185131	0.83[ASN][1000 genomes]
rs73185136	0.83[ASN][1000 genomes]
rs73185137	0.83[ASN][1000 genomes]
rs9637374	0.83[ASN][1000 genomes]
rs9637375	0.88[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9637376	0.83[ASN][1000 genomes]
rs9637377	0.89[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105073400-105084400	Weak transcription	Aorta	Aorta
2	chr3:105074400-105083600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:105074800-105083000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:105076200-105083600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:105077400-105082800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr3:105077800-105083800	Enhancers	Osteobl	bone
7	chr3:105077800-105084000	Enhancers	HSMM	muscle
8	chr3:105078000-105083800	Enhancers	NHEK	skin
9	chr3:105078600-105084200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:105078600-105084400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr3:105078600-105084400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:105078600-105084800	Weak transcription	Hela-S3	cervix
13	chr3:105078800-105083000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:105079000-105084000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:105079000-105084400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:105079600-105084000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:105079800-105083200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:105080400-105083400	Enhancers	NH-A	brain
19	chr3:105080400-105084200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:105080600-105083800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:105081000-105082800	Enhancers	A549	lung
22	chr3:105081000-105084200	Enhancers	NHLF	lung
23	chr3:105081200-105082800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:105081200-105084000	Enhancers	HMEC	breast
25	chr3:105081400-105083800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:105081600-105083000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:105081600-105084400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:105081800-105084000	Enhancers	HUVEC	blood vessel
29	chr3:105082000-105082800	Weak transcription	NHDF-Ad	bronchial
30	chr3:105082000-105083800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:105082000-105084200	Weak transcription	HSMMtube	muscle
32	chr3:105082200-105082800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:105082200-105083600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:105082200-105083600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:105082200-105084200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:105082400-105083800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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