Variant report

Variant	rs7599894
Chromosome Location	chr2:153415664-153415665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153414198..153416670-chr2:153417650..153421153,3	K562	blood:
2	chr2:153409474..153412030-chr2:153412610..153415752,4	K562	blood:
3	chr2:153413092..153415928-chr2:153423852..153428120,4	K562	blood:
4	chr2:153377943..153379745-chr2:153415461..153418420,2	K562	blood:
5	chr2:153414828..153416670-chr2:153417650..153420201,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10497106	0.84[MEX][hapmap];0.81[TSI][hapmap]
rs10497107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs10497108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.98[EUR][1000 genomes]
rs10497111	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]
rs11678890	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11892222	0.92[EUR][1000 genomes]
rs13002771	0.82[JPT][hapmap]
rs1370500	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1370501	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16823807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs16823809	0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs16823813	0.92[EUR][1000 genomes]
rs16831392	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]
rs16831399	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]
rs16831410	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs16831413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][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]
rs56220401	0.98[EUR][1000 genomes]
rs57173254	0.92[EUR][1000 genomes]
rs58383962	0.92[EUR][1000 genomes]
rs59103281	0.98[EUR][1000 genomes]
rs61698095	0.96[EUR][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]
rs7600114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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
rs7599894	MMADHC	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153399200-153427800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:153399400-153427600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:153399400-153429600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:153399600-153415800	Weak transcription	Aorta	Aorta
5	chr2:153400000-153415800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:153400000-153420800	Weak transcription	Hela-S3	cervix
7	chr2:153400000-153438000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:153400000-153468200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:153400600-153433400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:153400600-153442000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:153401600-153417400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:153402200-153427400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:153402400-153427000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:153403200-153448000	Weak transcription	Lung	lung
15	chr2:153403600-153418800	Weak transcription	Fetal Intestine Large	intestine
16	chr2:153404000-153415800	Weak transcription	Fetal Intestine Small	intestine
17	chr2:153404200-153442400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:153404400-153415800	Weak transcription	Fetal Stomach	stomach
19	chr2:153404800-153420000	Weak transcription	Esophagus	oesophagus
20	chr2:153404800-153425800	Weak transcription	Gastric	stomach
21	chr2:153405000-153416000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:153405200-153415800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:153405200-153415800	Weak transcription	Left Ventricle	heart
24	chr2:153405200-153441800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:153405400-153417400	Weak transcription	Adipose Nuclei	Adipose
26	chr2:153405400-153418800	Weak transcription	Ovary	ovary
27	chr2:153406200-153422800	Weak transcription	Fetal Kidney	kidney
28	chr2:153406400-153416000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:153407200-153417800	Weak transcription	Stomach Mucosa	stomach
30	chr2:153407600-153437800	Weak transcription	Pancreas	Pancrea
31	chr2:153409200-153415800	Enhancers	Brain Cingulate Gyrus	brain
32	chr2:153409200-153416400	Enhancers	Brain Substantia Nigra	brain
33	chr2:153409200-153417600	Enhancers	Brain Hippocampus Middle	brain
34	chr2:153411200-153416400	Enhancers	Brain Angular Gyrus	brain
35	chr2:153411400-153417000	Enhancers	Brain Anterior Caudate	brain
36	chr2:153411600-153416400	Weak transcription	A549	lung
37	chr2:153411800-153418400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:153412000-153416400	Enhancers	Fetal Muscle Leg	muscle
39	chr2:153412200-153418400	Weak transcription	Small Intestine	intestine
40	chr2:153412600-153418000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:153413200-153416400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:153413600-153417800	Enhancers	Osteobl	bone
43	chr2:153413800-153416800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:153413800-153417800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:153413800-153418000	Enhancers	NHDF-Ad	bronchial
46	chr2:153413800-153422000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:153414000-153417400	Weak transcription	Psoas Muscle	Psoas
48	chr2:153414000-153417600	Enhancers	NH-A	brain
49	chr2:153414000-153417600	Enhancers	NHLF	lung
50	chr2:153414000-153418800	Enhancers	Fetal Brain Male	brain

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