Variant report

Variant	rs1628116
Chromosome Location	chr12:104940562-104940563
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104939073..104940663-chr12:104943081..104945935,2	K562	blood:
2	chr12:104938513..104940949-chr12:104944779..104947009,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1005922	0.87[YRI][hapmap];0.93[AFR][1000 genomes]
rs11613208	0.94[ASW][hapmap];0.96[CEU][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap]
rs12829137	0.82[CHB][hapmap]
rs12829561	0.82[CHB][hapmap]
rs1553836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553839	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1625417	0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1626422	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704889	0.82[CHB][hapmap]
rs1704903	0.81[ASW][hapmap];0.96[CEU][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1704905	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1704915	0.91[EUR][1000 genomes]
rs1704916	0.96[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1704917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704918	0.96[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1704921	0.96[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs1704922	0.96[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs1704924	0.96[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs1704925	0.96[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs1704926	0.96[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1704927	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs1704929	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1795851	0.96[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1795852	0.96[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs1795853	0.96[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs1795854	0.96[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1795855	0.96[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1795856	0.92[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1795857	0.96[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1795859	0.96[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1795861	0.92[EUR][1000 genomes]
rs1795862	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1795864	1.00[CHB][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1795865	0.89[ASN][1000 genomes]
rs1795867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795868	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1973589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055861	0.96[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2141861	0.95[AFR][1000 genomes]
rs2665739	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs2665748	0.81[ASW][hapmap];0.96[CEU][hapmap];0.98[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2706273	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs313325	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs6539157	0.93[AFR][1000 genomes]
rs6539158	0.93[AFR][1000 genomes]
rs6539159	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs6539160	0.93[AFR][1000 genomes]
rs7968613	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs907097	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][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	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1628116	GOLGA2B	cis	parietal	SCAN
rs1628116	UTP20	cis	cerebellum	SCAN
rs1628116	KIAA1033	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104927200-104943000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:104929200-104942800	Weak transcription	Pancreas	Pancrea
3	chr12:104930200-104957600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:104930800-104940800	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:104930800-104943800	Weak transcription	Small Intestine	intestine
6	chr12:104933600-104941600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:104935200-104947400	Weak transcription	Aorta	Aorta
8	chr12:104935400-104943000	Weak transcription	A549	lung
9	chr12:104935400-104946400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:104935400-104947000	Weak transcription	Primary T cells from cord blood	blood
11	chr12:104935800-104940600	Weak transcription	Brain Anterior Caudate	brain
12	chr12:104935800-104943800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:104937000-104941000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:104938400-104943200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:104938600-104940600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:104938600-104941200	Enhancers	Primary T cells fromperipheralblood	blood
17	chr12:104938600-104941200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr12:104938600-104941600	Enhancers	Primary hematopoietic stem cells	blood
19	chr12:104938600-104944000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr12:104938800-104940800	Genic enhancers	Dnd41	blood
21	chr12:104938800-104941200	Enhancers	Placenta	Placenta
22	chr12:104939000-104940800	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr12:104939000-104941000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr12:104939000-104941200	Enhancers	Thymus	Thymus
25	chr12:104939000-104941400	Enhancers	Fetal Thymus	thymus
26	chr12:104939000-104941400	Enhancers	Lung	lung
27	chr12:104939000-104941800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:104939000-104942000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:104939000-104946600	Enhancers	Primary B cells from peripheral blood	blood
30	chr12:104939200-104941400	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr12:104939200-104943800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:104939200-104943800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:104939200-104944800	Weak transcription	Brain Germinal Matrix	brain
34	chr12:104939200-104945400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:104939200-104951200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:104939400-104941000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:104939400-104945000	Weak transcription	HSMMtube	muscle
38	chr12:104939600-104940600	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr12:104939600-104941600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:104939800-104940800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:104939800-104941200	Enhancers	Brain Hippocampus Middle	brain
42	chr12:104939800-104943600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:104939800-104945200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:104939800-104946600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:104939800-104947400	Weak transcription	Spleen	Spleen
46	chr12:104939800-104948000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:104939800-104948000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:104940200-104940600	Enhancers	K562	blood
49	chr12:104940200-104941000	Enhancers	Primary B cells from cord blood	blood
50	chr12:104940200-104941400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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