Variant report

Variant	rs41178
Chromosome Location	chr22:30440533-30440534
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	chr22:30431981..30436228-chr22:30436988..30442132,5	MCF-7	breast:
2	chr22:30438959..30441360-chr22:30444490..30446436,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12537	0.88[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2412960	0.83[CEU][hapmap]
rs2412963	0.83[CEU][hapmap]
rs28257	1.00[ASN][1000 genomes]
rs36600	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs36604	0.83[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap]
rs3788423	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs3887275	0.83[CEU][hapmap]
rs41162	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs41164	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs41172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41175	1.00[ASN][1000 genomes]
rs41177	0.92[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs41179	1.00[ASN][1000 genomes]
rs4239932	0.83[CEU][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs4337577	0.81[ASN][1000 genomes]
rs4823063	0.83[CEU][hapmap]
rs4823070	0.81[ASN][1000 genomes]
rs718772	0.87[CEU][hapmap]
rs737909	0.83[CEU][hapmap];0.87[TSI][hapmap]
rs737912	0.83[CEU][hapmap]
rs7510705	0.81[ASN][1000 genomes]
rs8141404	0.87[CEU][hapmap]
rs9620943	0.95[ASN][1000 genomes]
rs9625919	0.87[CEU][hapmap]
rs9625921	0.92[CEU][hapmap]

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	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs41178	NEFH	cis	cerebellum	SCAN
rs41178	ASCC2	cis	cerebellum	SCAN
rs41178	LIF	cis	cerebellum	SCAN
rs41178	CRYBB3	cis	parietal	SCAN
rs41178	ASPHD2	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30423600-30447600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr22:30424800-30443000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr22:30425800-30442000	Weak transcription	Fetal Brain Female	brain
4	chr22:30426600-30443000	Weak transcription	Thymus	Thymus
5	chr22:30430200-30442800	Weak transcription	Spleen	Spleen
6	chr22:30430200-30449600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr22:30432800-30440800	Weak transcription	Fetal Stomach	stomach
8	chr22:30435000-30440600	Weak transcription	Lung	lung
9	chr22:30435000-30450600	Weak transcription	Gastric	stomach
10	chr22:30436800-30440600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr22:30437000-30443400	Weak transcription	Esophagus	oesophagus
12	chr22:30438200-30448200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:30438800-30440600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr22:30438800-30440800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr22:30438800-30441000	Enhancers	HUVEC	blood vessel
16	chr22:30438800-30441800	Enhancers	Fetal Intestine Large	intestine
17	chr22:30439200-30441200	Enhancers	NHDF-Ad	bronchial
18	chr22:30439200-30441400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr22:30439200-30441400	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr22:30439400-30441600	Enhancers	Duodenum Mucosa	Duodenum
21	chr22:30439400-30441800	Enhancers	Fetal Intestine Small	intestine
22	chr22:30439600-30441000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr22:30439600-30441000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr22:30439600-30441000	Enhancers	HMEC	breast
25	chr22:30439600-30441000	Enhancers	NH-A	brain
26	chr22:30439600-30441000	Enhancers	NHLF	lung
27	chr22:30439600-30441200	Enhancers	NHEK	skin
28	chr22:30439600-30441400	Enhancers	Adipose Nuclei	Adipose
29	chr22:30439600-30442200	Enhancers	Stomach Mucosa	stomach
30	chr22:30439800-30440800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr22:30439800-30440800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr22:30439800-30441000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr22:30439800-30441000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr22:30439800-30441000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr22:30439800-30441000	Enhancers	HSMM	muscle
36	chr22:30439800-30441000	Enhancers	Osteobl	bone
37	chr22:30439800-30441200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr22:30439800-30441200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr22:30439800-30441200	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr22:30439800-30441600	Enhancers	Pancreas	Pancrea
41	chr22:30440000-30440600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr22:30440000-30440800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr22:30440000-30441000	Enhancers	Fetal Lung	lung
44	chr22:30440000-30441200	Enhancers	HSMMtube	muscle
45	chr22:30440200-30440600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr22:30440200-30440600	Enhancers	A549	lung
47	chr22:30440200-30441200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr22:30440200-30441200	Weak transcription	Fetal Muscle Leg	muscle
49	chr22:30440400-30440600	Enhancers	HepG2	liver
50	chr22:30440400-30440800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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