Variant report

Variant	rs16831392
Chromosome Location	chr2:153434952-153434953
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10497106	0.92[MEX][hapmap]
rs10497107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497108	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497111	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678890	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11892222	0.95[EUR][1000 genomes]
rs13002771	0.82[JPT][hapmap]
rs1370500	0.88[EUR][1000 genomes]
rs1370501	0.85[EUR][1000 genomes]
rs16823807	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823809	0.84[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16823813	0.95[EUR][1000 genomes]
rs16831399	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831410	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17327752	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap]
rs17399648	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2678299	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs3811572	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56220401	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57173254	0.95[EUR][1000 genomes]
rs58383962	0.95[EUR][1000 genomes]
rs59103281	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60447103	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs61698095	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434081	0.82[JPT][hapmap]
rs6706231	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6749146	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6760321	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap]
rs7573833	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7599894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs7600114	0.98[EUR][1000 genomes]
rs9753431	1.00[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16831392	MMADHC	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153400000-153438000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:153400000-153468200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:153400600-153442000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:153403200-153448000	Weak transcription	Lung	lung
5	chr2:153404200-153442400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:153405200-153441800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:153407600-153437800	Weak transcription	Pancreas	Pancrea
8	chr2:153415000-153436800	Weak transcription	HUVEC	blood vessel
9	chr2:153415000-153438200	Weak transcription	Fetal Lung	lung
10	chr2:153416400-153438000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:153416400-153454200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:153416400-153465200	Weak transcription	Left Ventricle	heart
13	chr2:153417800-153442000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:153418200-153437400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:153418800-153444600	Weak transcription	Fetal Brain Male	brain
16	chr2:153419200-153437400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:153419600-153438000	Weak transcription	Fetal Intestine Large	intestine
18	chr2:153420400-153443400	Weak transcription	Fetal Intestine Small	intestine
19	chr2:153423800-153471200	Weak transcription	Fetal Kidney	kidney
20	chr2:153425200-153438000	Weak transcription	Fetal Brain Female	brain
21	chr2:153425600-153438200	Enhancers	Brain Hippocampus Middle	brain
22	chr2:153428000-153436800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:153428000-153436800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:153428000-153438000	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:153428000-153442000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:153428000-153468200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:153428200-153440000	Weak transcription	Fetal Heart	heart
28	chr2:153428200-153456000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:153428400-153437400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:153428400-153437800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr2:153428400-153437800	Weak transcription	Adipose Nuclei	Adipose
32	chr2:153429200-153456200	Weak transcription	Spleen	Spleen
33	chr2:153429600-153442200	Strong transcription	HepG2	liver
34	chr2:153429800-153437800	Weak transcription	HSMMtube	muscle
35	chr2:153429800-153439600	Weak transcription	A549	lung
36	chr2:153430000-153440200	Weak transcription	NH-A	brain
37	chr2:153430000-153449400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:153430200-153436400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:153430200-153436800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:153430200-153437200	Weak transcription	HMEC	breast
41	chr2:153430200-153437400	Weak transcription	HSMM	muscle
42	chr2:153430200-153438000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:153430200-153440800	Weak transcription	NHLF	lung
44	chr2:153430400-153441200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:153431400-153438000	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr2:153431600-153437800	Weak transcription	NHDF-Ad	bronchial
47	chr2:153432400-153436000	Enhancers	Brain Anterior Caudate	brain
48	chr2:153433000-153435400	Weak transcription	Placenta	Placenta
49	chr2:153433200-153436400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:153433400-153438600	Enhancers	Brain Cingulate Gyrus	brain

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