Variant report

Variant	rs10497108
Chromosome Location	chr2:153438438-153438439
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153429587..153431240-chr2:153437990..153439692,2	K562	blood:
2	chr2:153437360..153438992-chr2:153441659..153443672,2	MCF-7	breast:
3	chr2:153431363..153434318-chr2:153436481..153440010,3	K562	blood:
4	chr2:153438032..153440422-chr2:153459434..153461686,2	MCF-7	breast:

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];0.92[YRI][hapmap];0.98[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];0.96[TSI][hapmap];0.92[YRI][hapmap];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];0.81[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823809	0.84[MEX][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs16823813	0.95[EUR][1000 genomes]
rs16831392	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]
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];0.96[TSI][hapmap];0.92[YRI][hapmap];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];1.00[YRI][hapmap];0.96[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	0.95[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	0.87[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];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];0.89[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
rs10497108	MMADHC	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153400000-153468200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:153400600-153442000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:153403200-153448000	Weak transcription	Lung	lung
4	chr2:153404200-153442400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:153405200-153441800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:153416400-153454200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:153416400-153465200	Weak transcription	Left Ventricle	heart
8	chr2:153417800-153442000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:153418800-153444600	Weak transcription	Fetal Brain Male	brain
10	chr2:153420400-153443400	Weak transcription	Fetal Intestine Small	intestine
11	chr2:153423800-153471200	Weak transcription	Fetal Kidney	kidney
12	chr2:153428000-153442000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:153428000-153468200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:153428200-153440000	Weak transcription	Fetal Heart	heart
15	chr2:153428200-153456000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:153429200-153456200	Weak transcription	Spleen	Spleen
17	chr2:153429600-153442200	Strong transcription	HepG2	liver
18	chr2:153429800-153439600	Weak transcription	A549	lung
19	chr2:153430000-153440200	Weak transcription	NH-A	brain
20	chr2:153430000-153449400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:153430200-153440800	Weak transcription	NHLF	lung
22	chr2:153430400-153441200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:153433400-153438600	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:153434200-153442600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:153434200-153473600	Weak transcription	Brain Germinal Matrix	brain
26	chr2:153434400-153439600	Weak transcription	Aorta	Aorta
27	chr2:153434400-153440000	Weak transcription	Psoas Muscle	Psoas
28	chr2:153434400-153442000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:153434400-153454400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:153434600-153442000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:153434600-153442400	Weak transcription	Small Intestine	intestine
32	chr2:153434800-153441400	Weak transcription	Ovary	ovary
33	chr2:153435200-153441600	Enhancers	Brain Substantia Nigra	brain
34	chr2:153435400-153473200	Weak transcription	Right Ventricle	heart
35	chr2:153435600-153455200	Weak transcription	Hela-S3	cervix
36	chr2:153436400-153438600	Enhancers	Brain Angular Gyrus	brain
37	chr2:153436600-153444800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr2:153436800-153438600	Enhancers	Osteobl	bone
39	chr2:153437400-153438600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:153437400-153438600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr2:153437400-153439000	Strong transcription	Fetal Stomach	stomach
42	chr2:153437400-153441200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:153437400-153441200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:153437600-153438600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:153437600-153439600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:153437800-153439000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:153437800-153439000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:153437800-153439000	Strong transcription	Placenta	Placenta
49	chr2:153437800-153439800	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:153437800-153439800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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