Variant report

Variant	rs41176
Chromosome Location	chr22:30432403-30432404
allele	A/C
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	chr22:30422072..30424953-chr22:30431511..30433741,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1076135	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs1468176	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1548389	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1807711	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs193471	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs193474	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs193475	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs193476	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1989870	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2007446	0.91[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2007458	0.92[CEU][hapmap]
rs2285667	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2301402	0.92[CEU][hapmap]
rs2412970	0.81[JPT][hapmap]
rs2412972	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2412976	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs41156	0.82[EUR][1000 genomes]
rs41157	0.82[EUR][1000 genomes]
rs41161	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41165	0.92[CEU][hapmap]
rs41168	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs41170	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs41171	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs41173	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4336042	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4820827	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4823076	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5752975	0.92[CEU][hapmap]
rs5752978	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap]
rs5753008	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753025	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753037	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5763614	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs5763670	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5763751	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763775	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5763779	1.00[CEU][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5763790	0.85[AMR][1000 genomes]
rs5763842	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59663694	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5997579	0.81[JPT][hapmap]
rs7287570	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73162764	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73164755	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs737911	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs757024	0.81[JPT][hapmap]
rs9306468	1.00[CEU][hapmap]
rs960987	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs997913	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
rs41176	NEFH	cis	cerebellum	SCAN
rs41176	ASCC2	cis	cerebellum	SCAN
rs41176	CABP7	cis	cerebellum	SCAN
rs41176	MTMR3	cis	parietal	SCAN
rs41176	TTC28AS	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30390200-30434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30391400-30433000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr22:30409000-30432800	Strong transcription	Fetal Stomach	stomach
4	chr22:30419600-30434400	Weak transcription	Small Intestine	intestine
5	chr22:30422400-30434200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr22:30422400-30434200	Weak transcription	HUVEC	blood vessel
7	chr22:30423000-30432600	Weak transcription	NH-A	brain
8	chr22:30423400-30434400	Weak transcription	A549	lung
9	chr22:30423600-30447600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr22:30424200-30434000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr22:30424600-30432600	Weak transcription	HMEC	breast
12	chr22:30424600-30435600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr22:30424800-30443000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr22:30425000-30434200	Weak transcription	Gastric	stomach
15	chr22:30425200-30434000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr22:30425200-30434200	Weak transcription	Pancreas	Pancrea
17	chr22:30425200-30434200	Weak transcription	NHLF	lung
18	chr22:30425200-30435800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr22:30425200-30438800	Weak transcription	Fetal Intestine Large	intestine
20	chr22:30425200-30440000	Weak transcription	Fetal Lung	lung
21	chr22:30425200-30440200	Weak transcription	Brain Germinal Matrix	brain
22	chr22:30425600-30439400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr22:30425800-30433000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr22:30425800-30433800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr22:30425800-30434000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr22:30425800-30434800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr22:30425800-30435400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr22:30425800-30439800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr22:30425800-30442000	Weak transcription	Fetal Brain Female	brain
30	chr22:30426000-30434400	Weak transcription	Left Ventricle	heart
31	chr22:30426200-30434000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr22:30426200-30434200	Weak transcription	Lung	lung
33	chr22:30426600-30443000	Weak transcription	Thymus	Thymus
34	chr22:30427600-30432600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr22:30429200-30434200	Weak transcription	Psoas Muscle	Psoas
36	chr22:30429400-30439800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr22:30429800-30433000	Weak transcription	Ovary	ovary
38	chr22:30429800-30434600	Weak transcription	Right Atrium	heart
39	chr22:30429800-30435000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr22:30430200-30432800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr22:30430200-30434000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr22:30430200-30434000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr22:30430200-30442800	Weak transcription	Spleen	Spleen
44	chr22:30430200-30449600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr22:30430400-30433600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr22:30430400-30434400	Weak transcription	Liver	Liver
47	chr22:30430400-30434400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr22:30430400-30435800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr22:30430800-30436200	Weak transcription	Fetal Muscle Trunk	muscle
50	chr22:30430800-30439400	Weak transcription	Fetal Intestine Small	intestine

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