Variant report

Variant	rs6788786
Chromosome Location	chr3:179396069-179396070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:179391443..179393801-chr3:179394734..179396549,3	MCF-7	breast:
2	chr3:179391169..179394012-chr3:179395352..179397041,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs13097252	0.87[ASN][1000 genomes]
rs13322033	0.95[ASN][1000 genomes]
rs13326216	0.91[ASN][1000 genomes]
rs2268941	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2268942	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs34161332	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854945	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771840	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6785332	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6797965	1.00[CHB][hapmap]
rs6807974	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7629853	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs9810165	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9810460	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9859059	0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4140	chr3:179383961-179429704	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6788786	MCCC1	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179372600-179403200	Weak transcription	Primary B cells from cord blood	blood
2	chr3:179372600-179408400	Weak transcription	Fetal Intestine Small	intestine
3	chr3:179372600-179425200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:179374600-179408000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:179376600-179400800	Weak transcription	Dnd41	blood
6	chr3:179380600-179418800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:179384400-179410400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:179384600-179397600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:179384800-179402200	Weak transcription	Fetal Stomach	stomach
10	chr3:179384800-179406200	Weak transcription	HSMM	muscle
11	chr3:179384800-179408000	Weak transcription	Fetal Thymus	thymus
12	chr3:179384800-179415200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:179384800-179425000	Weak transcription	Brain Anterior Caudate	brain
14	chr3:179384800-179428400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:179384800-179443800	Weak transcription	Esophagus	oesophagus
16	chr3:179385000-179398800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:179385000-179415600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:179385000-179439200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:179385000-179448400	Weak transcription	Fetal Brain Male	brain
20	chr3:179385400-179419000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:179385600-179405400	Weak transcription	Fetal Brain Female	brain
22	chr3:179386000-179398800	Weak transcription	Brain Germinal Matrix	brain
23	chr3:179388600-179398800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:179389600-179399600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:179390000-179400200	Weak transcription	NHLF	lung
26	chr3:179390600-179403400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr3:179390800-179408000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:179391000-179403600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:179391000-179444000	Weak transcription	Pancreas	Pancrea
30	chr3:179391000-179452200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:179391200-179396400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:179391200-179399600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:179391400-179398400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:179391400-179403600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:179391400-179404600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:179391400-179415400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:179391400-179426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:179391400-179439200	Weak transcription	NHEK	skin
39	chr3:179391600-179396400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:179391600-179397800	Weak transcription	Ovary	ovary
41	chr3:179391600-179398800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:179391600-179399000	Weak transcription	Right Ventricle	heart
43	chr3:179391600-179399200	Weak transcription	Lung	lung
44	chr3:179391600-179403600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:179391600-179408200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:179391600-179412800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:179391600-179424000	Weak transcription	Hela-S3	cervix
48	chr3:179391800-179398400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:179392200-179396200	Weak transcription	Left Ventricle	heart
50	chr3:179392200-179398400	Weak transcription	Right Atrium	heart

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