Variant report

Variant	rs312163
Chromosome Location	chr12:105125397-105125398
allele	A/G
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:105119240..105120863-chr12:105125157..105128000,2	K562	blood:
2	chr12:105124334..105127781-chr12:105128206..105132825,4	K562	blood:
3	chr12:105124445..105127183-chr12:105135095..105137276,2	K562	blood:
4	chr12:105118825..105122696-chr12:105123025..105128000,6	K562	blood:
5	chr12:105114220..105116459-chr12:105123813..105125766,2	K562	blood:
6	chr12:105123345..105125834-chr12:105127329..105130325,2	K562	blood:
7	chr12:105121311..105124044-chr12:105125016..105127574,2	MCF-7	breast:

No data

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11112176	0.89[ASN][1000 genomes]
rs11112178	0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs12230941	0.82[ASN][1000 genomes]
rs12426228	0.85[CHD][hapmap]
rs2559634	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2694420	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs312149	0.81[EUR][1000 genomes]
rs312150	0.81[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs312151	0.81[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs312154	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs312155	0.88[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs312157	0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs312158	0.86[EUR][1000 genomes]
rs312160	0.81[CEU][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs312161	0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs312162	0.81[CEU][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs312165	0.86[CEU][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs312166	0.82[ASW][hapmap];0.85[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs312167	0.83[ASW][hapmap];0.85[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs312168	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs312169	0.88[CEU][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs312171	0.84[CEU][hapmap]
rs60756405	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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs312163	SLC5A8	cis	cerebellum	SCAN
rs312163	NT5DC3	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105080400-105131800	Weak transcription	NHEK	skin
2	chr12:105114400-105125800	Weak transcription	Fetal Brain Female	brain
3	chr12:105115000-105129800	Weak transcription	Fetal Lung	lung
4	chr12:105115200-105129600	Weak transcription	Placenta	Placenta
5	chr12:105115400-105128800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:105115600-105128400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:105116000-105125800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:105116000-105131600	Weak transcription	Esophagus	oesophagus
9	chr12:105116200-105126400	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:105116600-105128400	Weak transcription	A549	lung
11	chr12:105116800-105125800	Weak transcription	Primary T cells from cord blood	blood
12	chr12:105116800-105126400	Weak transcription	Brain Germinal Matrix	brain
13	chr12:105117000-105125800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:105117000-105127000	Strong transcription	Dnd41	blood
15	chr12:105117200-105126400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:105117400-105126400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:105117400-105127400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:105117400-105127600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:105117600-105126600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:105117600-105126800	Weak transcription	Thymus	Thymus
21	chr12:105117800-105129400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr12:105117800-105129400	Weak transcription	GM12878-XiMat	blood
23	chr12:105118000-105125600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:105118400-105131000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:105120200-105130000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:105121200-105125600	Enhancers	Fetal Muscle Leg	muscle
27	chr12:105121400-105125600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:105121400-105126600	Weak transcription	Gastric	stomach
29	chr12:105121400-105129800	Weak transcription	Pancreas	Pancrea
30	chr12:105121800-105130800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:105123000-105127000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:105123000-105128600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:105123200-105126400	Weak transcription	Fetal Thymus	thymus
34	chr12:105123200-105127800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:105123400-105126800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr12:105123400-105136200	Enhancers	Primary T cells fromperipheralblood	blood
37	chr12:105124000-105127200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:105124000-105134400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:105124200-105125400	Enhancers	Fetal Stomach	stomach
40	chr12:105124400-105126800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:105124400-105130600	Weak transcription	Primary B cells from cord blood	blood
42	chr12:105124600-105125400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr12:105124600-105125800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:105124600-105128200	Weak transcription	Spleen	Spleen
45	chr12:105124600-105129000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr12:105124600-105131600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr12:105124800-105127000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr12:105124800-105129800	Weak transcription	Fetal Intestine Small	intestine
49	chr12:105124800-105133600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr12:105125000-105126400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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