Variant report

Variant	rs41168
Chromosome Location	chr22:30418161-30418162
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1076135	0.85[CEU][hapmap]
rs1468176	0.90[AFR][1000 genomes]
rs1548389	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs193474	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs193475	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs193476	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1989870	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2007446	0.91[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2007458	0.92[CEU][hapmap]
rs2285667	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2301402	0.92[CEU][hapmap]
rs2412972	0.87[AFR][1000 genomes]
rs2412976	0.81[AFR][1000 genomes]
rs41155	0.82[EUR][1000 genomes]
rs41156	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41157	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41161	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41165	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs41170	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41173	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41176	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4336042	0.87[AFR][1000 genomes]
rs4823076	0.86[AFR][1000 genomes]
rs5752975	0.92[CEU][hapmap]
rs5752978	1.00[CEU][hapmap]
rs5753025	0.90[AFR][1000 genomes]
rs5763670	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5763751	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs5763775	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs5763779	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs59663694	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7287570	0.92[AFR][1000 genomes]
rs73162764	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs737911	0.96[CEU][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9306465	0.92[CEU][hapmap]
rs9306468	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.82[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
rs41168	NEFH	cis	cerebellum	SCAN
rs41168	MTMR3	cis	parietal	SCAN
rs41168	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs41168	CABP7	cis	cerebellum	SCAN
rs41168	ASCC2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30363400-30427800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr22:30367000-30426600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr22:30390200-30434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr22:30391400-30433000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr22:30392600-30425000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr22:30393800-30424800	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr22:30394600-30424600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr22:30394800-30425200	Strong transcription	Fetal Intestine Large	intestine
9	chr22:30394800-30426200	Strong transcription	Placenta	Placenta
10	chr22:30396800-30426200	Strong transcription	Primary B cells from cord blood	blood
11	chr22:30397600-30419800	Strong transcription	Dnd41	blood
12	chr22:30397800-30423800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr22:30397800-30425400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr22:30398000-30424400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr22:30398000-30426200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr22:30398400-30425000	Strong transcription	Primary hematopoietic stem cells	blood
17	chr22:30398600-30425200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr22:30399800-30422400	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr22:30401200-30420000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr22:30401200-30423200	Strong transcription	Adipose Nuclei	Adipose
21	chr22:30401600-30425200	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr22:30402000-30422600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr22:30402000-30422600	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr22:30402200-30425200	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr22:30402400-30420800	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr22:30402400-30424600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr22:30402600-30423600	Strong transcription	Liver	Liver
28	chr22:30402600-30426200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr22:30402800-30424200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr22:30402800-30425800	Strong transcription	Fetal Muscle Leg	muscle
31	chr22:30403000-30421000	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr22:30403000-30424400	Strong transcription	Fetal Brain Female	brain
33	chr22:30403000-30425200	Strong transcription	Stomach Smooth Muscle	stomach
34	chr22:30404000-30423400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr22:30404400-30420800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr22:30404400-30426400	Strong transcription	Primary T cells from cord blood	blood
37	chr22:30404800-30426000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr22:30405000-30424200	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr22:30405200-30424600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr22:30405200-30424800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr22:30405800-30424800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr22:30406000-30426600	Strong transcription	Thymus	Thymus
43	chr22:30406200-30425200	Strong transcription	Fetal Thymus	thymus
44	chr22:30407800-30425200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr22:30408000-30425800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr22:30408200-30418400	Strong transcription	Gastric	stomach
47	chr22:30408200-30420200	Strong transcription	Esophagus	oesophagus
48	chr22:30408200-30422800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr22:30408200-30422800	Strong transcription	Fetal Intestine Small	intestine
50	chr22:30408200-30425000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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