Variant report

Variant	rs12469386
Chromosome Location	chr2:178358281-178358282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178357170..178361167-chr2:178362670..178365419,4	K562	blood:
2	chr2:178355640..178358499-chr2:178381852..178383963,3	K562	blood:

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10165785	0.93[ASN][1000 genomes]
rs10170546	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10170667	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10194648	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10201153	0.85[JPT][hapmap]
rs10497501	0.89[CEU][hapmap];0.82[CHB][hapmap]
rs10497502	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10497503	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10497508	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10803909	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10930792	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10930798	0.80[EUR][1000 genomes]
rs11684320	0.80[EUR][1000 genomes]
rs11688684	0.85[JPT][hapmap]
rs11893448	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12104588	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12463893	0.80[EUR][1000 genomes]
rs12471741	0.80[EUR][1000 genomes]
rs12474344	0.80[JPT][hapmap]
rs12612857	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs12615367	0.85[JPT][hapmap]
rs12616093	0.85[JPT][hapmap]
rs12616443	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12618139	0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12622298	0.80[EUR][1000 genomes]
rs12693120	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12990594	0.85[JPT][hapmap]
rs12990729	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12996447	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13000048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13004955	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13013752	0.80[EUR][1000 genomes]
rs13022567	0.80[JPT][hapmap]
rs13027959	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1348848	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1348849	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1348850	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1374437	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1405713	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1453370	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1453373	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1548067	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs16865203	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs16865216	0.82[ASN][1000 genomes]
rs16865229	0.82[ASN][1000 genomes]
rs16865291	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs16865328	0.85[JPT][hapmap]
rs16865331	0.85[JPT][hapmap]
rs1901825	1.00[JPT][hapmap]
rs1901826	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs1901829	0.81[ASN][1000 genomes]
rs1975543	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1979058	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2034678	0.95[JPT][hapmap]
rs2060929	1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2084233	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2121430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2166558	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2197611	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364853	0.84[ASN][1000 genomes]
rs2364854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213945	0.85[JPT][hapmap]
rs3769995	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3769996	0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3769997	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3770002	0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3813259	1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3902850	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3927978	0.81[EUR][1000 genomes]
rs4243388	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4243390	0.80[EUR][1000 genomes]
rs4341974	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4528793	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4893821	0.81[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs4893822	1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4893823	1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4893824	0.93[ASN][1000 genomes]
rs4893825	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4893931	0.80[ASN][1000 genomes]
rs4893935	0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.88[MKK][hapmap];0.83[ASN][1000 genomes]
rs4893936	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4893938	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4893941	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4893944	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4893945	0.92[ASN][1000 genomes]
rs4893946	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4893950	1.00[CEU][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4893951	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4893954	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893957	1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4893959	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4893961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4893962	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4893965	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap]
rs57273542	0.82[ASN][1000 genomes]
rs57295810	0.86[ASN][1000 genomes]
rs57527255	0.85[ASN][1000 genomes]
rs57541536	0.85[ASN][1000 genomes]
rs57733896	0.85[ASN][1000 genomes]
rs57948641	0.85[ASN][1000 genomes]
rs58297927	0.85[ASN][1000 genomes]
rs59111239	0.82[ASN][1000 genomes]
rs59421055	0.83[ASN][1000 genomes]
rs59504156	0.83[ASN][1000 genomes]
rs60642012	0.83[ASN][1000 genomes]
rs60670838	0.82[ASN][1000 genomes]
rs6433670	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6433673	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6710575	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6742951	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6761593	0.82[EUR][1000 genomes]
rs7565022	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7573763	0.86[ASN][1000 genomes]
rs7586051	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7587604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7591807	1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7604673	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7606235	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7607450	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8941	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs952746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9679607	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9789582	0.89[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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12469386	DKFZp451M2119	Cis_1M	lymphoblastoid	RTeQTL
rs12469386	TTC30B	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178296400-178397000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr2:178331000-178361600	Weak transcription	Brain Substantia Nigra	brain
3	chr2:178331000-178378600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:178331200-178378600	Weak transcription	Placenta	Placenta
5	chr2:178331200-178379200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:178331400-178388400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:178331600-178385600	Weak transcription	Spleen	Spleen
8	chr2:178331800-178360600	Weak transcription	Lung	lung
9	chr2:178331800-178373800	Weak transcription	Gastric	stomach
10	chr2:178331800-178375800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:178331800-178375800	Weak transcription	Pancreas	Pancrea
12	chr2:178331800-178389400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:178332000-178392800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:178332000-178393800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:178335000-178410600	Weak transcription	Thymus	Thymus
16	chr2:178337600-178386200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:178338000-178403000	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:178339000-178359800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:178339800-178394400	Weak transcription	Hela-S3	cervix
20	chr2:178342400-178392000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:178342600-178391000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:178343800-178379400	Weak transcription	NHEK	skin
23	chr2:178343800-178391200	Weak transcription	HMEC	breast
24	chr2:178344000-178374000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:178344200-178371000	Weak transcription	A549	lung
26	chr2:178344800-178381200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:178345400-178360000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:178348000-178375000	Weak transcription	Adipose Nuclei	Adipose
29	chr2:178348400-178402600	Weak transcription	NHDF-Ad	bronchial
30	chr2:178349800-178374600	Weak transcription	Left Ventricle	heart
31	chr2:178349800-178377600	Weak transcription	Fetal Intestine Small	intestine
32	chr2:178349800-178378000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:178349800-178383400	Weak transcription	Fetal Stomach	stomach
34	chr2:178349800-178407800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:178350000-178362400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:178350000-178407000	Weak transcription	Osteobl	bone
37	chr2:178354000-178377400	Weak transcription	GM12878-XiMat	blood
38	chr2:178354600-178392000	Weak transcription	Brain Anterior Caudate	brain
39	chr2:178355000-178380600	Weak transcription	Fetal Heart	heart
40	chr2:178355000-178384400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:178355400-178359000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:178355800-178360200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr2:178355800-178360400	Strong transcription	HepG2	liver
44	chr2:178356000-178405400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:178356400-178360200	Strong transcription	Dnd41	blood
46	chr2:178356400-178384400	Weak transcription	Colon Smooth Muscle	Colon
47	chr2:178356600-178358600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:178356600-178358600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr2:178356600-178358800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:178356600-178358800	Strong transcription	Primary B cells from cord blood	blood

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