Variant report

Variant	rs12140800
Chromosome Location	chr1:179319816-179319817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179319158..179320695-chr1:179327831..179330357,2	K562	blood:
2	chr1:179314011..179316743-chr1:179317198..179320043,2	K562	blood:
3	chr1:179317813..179320620-chr1:179325439..179328200,3	MCF-7	breast:
4	chr1:179319218..179322738-chr1:179324103..179326545,3	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1044925	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10753193	0.82[CHD][hapmap]
rs10798666	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10913736	0.80[MKK][hapmap]
rs12024173	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2065761	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2152319	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];1.00[ASN][1000 genomes]
rs3753525	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.94[ASN][1000 genomes]
rs3753527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4360482	0.82[CHD][hapmap]
rs4606280	0.82[CHD][hapmap]
rs61821461	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425535	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6659294	0.82[CHD][hapmap]
rs6662859	0.82[CHD][hapmap]
rs6673985	0.96[CEU][hapmap];0.90[TSI][hapmap]
rs6675699	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7349152	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7536854	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7537139	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7548288	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7551027	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7556547	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[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	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv1804302	chr1:179315357-179333194	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12140800	AXDND1	cis	Thyroid	GTEx
rs12140800	TDRD5	cis	Artery Aorta	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179264800-179334200	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:179266400-179322800	Weak transcription	Small Intestine	intestine
3	chr1:179292400-179328000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:179293000-179322600	Weak transcription	Fetal Heart	heart
5	chr1:179294200-179324600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:179296800-179327800	Weak transcription	Colonic Mucosa	Colon
7	chr1:179297400-179321600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:179298600-179324200	Weak transcription	Thymus	Thymus
9	chr1:179300400-179334600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:179300600-179322400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:179301800-179322800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:179303200-179324600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:179303400-179322600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:179304200-179320000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:179304200-179324400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:179304200-179324400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr1:179304200-179324600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:179304200-179325200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:179304400-179324400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:179304600-179324200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:179305200-179327200	Weak transcription	Right Ventricle	heart
22	chr1:179305600-179334200	Weak transcription	Pancreas	Pancrea
23	chr1:179305800-179322600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:179306000-179321000	Strong transcription	Dnd41	blood
25	chr1:179306800-179324600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:179307400-179325800	Weak transcription	Esophagus	oesophagus
27	chr1:179307600-179322600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:179307600-179325200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:179307800-179322200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:179308000-179321000	Weak transcription	Fetal Brain Male	brain
31	chr1:179308000-179324400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:179308400-179322600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:179308600-179322000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:179308800-179320800	Strong transcription	Osteobl	bone
35	chr1:179309800-179326400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:179310000-179325200	Strong transcription	Primary T cells from cord blood	blood
37	chr1:179310200-179322000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:179310200-179323000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:179310400-179322800	Weak transcription	Aorta	Aorta
40	chr1:179310400-179324400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr1:179311200-179325200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:179311600-179320800	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:179311600-179326400	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr1:179311800-179321200	Strong transcription	Duodenum Mucosa	Duodenum
45	chr1:179312000-179324200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:179312000-179324800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:179312200-179322400	Weak transcription	HMEC	breast
48	chr1:179312200-179322600	Weak transcription	Stomach Mucosa	stomach
49	chr1:179312200-179325200	Strong transcription	Liver	Liver
50	chr1:179312600-179320800	Strong transcription	Rectal Mucosa Donor 31	rectum

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