Variant report

Variant	rs2258946
Chromosome Location	chr10:93624672-93624673
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:93583779..93585319-chr10:93624182..93625736,2	K562	blood:
2	chr10:93622435..93625235-chr10:93666219..93668406,2	MCF-7	breast:
3	chr10:93623670..93626355-chr10:93627411..93630158,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272817	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10736066	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359353	0.82[EUR][1000 genomes]
rs1417257	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1538831	0.82[EUR][1000 genomes]
rs1538832	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630388	0.82[EUR][1000 genomes]
rs17347260	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17433251	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770469	0.82[EUR][1000 genomes]
rs1770474	0.82[EUR][1000 genomes]
rs1772181	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1772186	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1772187	0.82[EUR][1000 genomes]
rs1772188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2259094	0.84[EUR][1000 genomes]
rs2259287	0.84[EUR][1000 genomes]
rs2259659	0.82[EUR][1000 genomes]
rs2260773	0.82[EUR][1000 genomes]
rs2261029	0.82[EUR][1000 genomes]
rs2261035	0.82[EUR][1000 genomes]
rs2421705	1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2421706	1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61743258	0.81[ASN][1000 genomes]
rs61874701	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61874749	0.81[ASN][1000 genomes]
rs61876142	0.81[ASN][1000 genomes]
rs61876148	0.81[ASN][1000 genomes]
rs61876151	0.81[ASN][1000 genomes]
rs6583790	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6583792	1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7083959	0.82[EUR][1000 genomes]
rs7089495	0.81[ASW][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7093658	0.89[ASW][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs72823110	0.81[ASN][1000 genomes]
rs72823162	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7912830	0.81[ASW][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7917198	0.81[ASN][1000 genomes]
rs7917450	0.81[ASN][1000 genomes]
rs7919191	0.80[EUR][1000 genomes]
rs9420573	0.82[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2258946	TNKS2	cis	Thyroid	GTEx
rs2258946	IFIT2	cis	parietal	SCAN
rs2258946	TNKS2	cis	Artery Aorta	GTEx
rs2258946	NOC3L	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93569200-93626800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:93570800-93625000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr10:93570800-93626000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr10:93570800-93626000	Strong transcription	Dnd41	blood
5	chr10:93571000-93625800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr10:93571200-93626400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr10:93571400-93626400	Strong transcription	Liver	Liver
8	chr10:93571400-93626400	Strong transcription	Fetal Thymus	thymus
9	chr10:93572000-93626200	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr10:93572000-93626400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr10:93572000-93626400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:93572200-93625600	Strong transcription	Placenta	Placenta
13	chr10:93572200-93626400	Strong transcription	Primary B cells from cord blood	blood
14	chr10:93572400-93624800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr10:93572400-93626000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr10:93572400-93626000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr10:93572400-93626000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr10:93572400-93626200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr10:93572400-93626200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:93572600-93626200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr10:93572600-93626200	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr10:93572600-93626200	Strong transcription	Adipose Nuclei	Adipose
23	chr10:93572600-93626600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:93572600-93629000	Weak transcription	Stomach Mucosa	stomach
25	chr10:93572800-93626200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr10:93573000-93626200	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr10:93577000-93624800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr10:93584200-93626400	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr10:93585400-93626200	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr10:93591800-93626200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr10:93598400-93629000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr10:93599200-93629000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr10:93599600-93634600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:93605600-93625600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr10:93606400-93625400	Weak transcription	Spleen	Spleen
36	chr10:93606400-93630200	Weak transcription	Esophagus	oesophagus
37	chr10:93608200-93625800	Strong transcription	HSMM	muscle
38	chr10:93608800-93627400	Weak transcription	Pancreas	Pancrea
39	chr10:93608800-93627600	Weak transcription	Gastric	stomach
40	chr10:93608800-93639200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr10:93608800-93643400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr10:93610600-93627600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr10:93612200-93624800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr10:93612200-93627600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr10:93613400-93627800	Weak transcription	Aorta	Aorta
46	chr10:93613600-93625200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr10:93613600-93627400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr10:93615200-93626000	Strong transcription	HMEC	breast
49	chr10:93615400-93627000	Weak transcription	Fetal Intestine Small	intestine
50	chr10:93616800-93625600	Weak transcription	K562	blood

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