Variant report

Variant	rs41157
Chromosome Location	chr22:30405151-30405152
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30403877..30405549-chr22:30406333..30408441,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LIF-2	chr22:30404731-30405185	ENSG00000227117.2
2	lnc-LIF-2	chr22:30404830-30405185	NONHSAT084746
3	lnc-LIF-2	chr22:30404731-30405185	NR_110541

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1076135	0.85[CEU][hapmap]
rs1548389	1.00[CEU][hapmap]
rs1807508	0.83[EUR][1000 genomes]
rs1894473	1.00[YRI][hapmap]
rs193475	0.80[EUR][1000 genomes]
rs193476	0.81[EUR][1000 genomes]
rs1989870	0.81[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap]
rs2007446	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2007458	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2074707	0.89[CEU][hapmap]
rs2285667	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2301402	0.92[CEU][hapmap]
rs3788420	0.83[EUR][1000 genomes]
rs41155	0.90[EUR][1000 genomes]
rs41156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41159	0.85[EUR][1000 genomes]
rs41161	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41165	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs41168	0.91[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41170	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41171	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41173	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41176	0.82[EUR][1000 genomes]
rs5752964	0.89[CEU][hapmap];0.86[TSI][hapmap]
rs5752975	0.92[CEU][hapmap]
rs5752978	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs5752992	0.83[EUR][1000 genomes]
rs5763512	0.89[CEU][hapmap]
rs5763614	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs5763645	0.81[EUR][1000 genomes]
rs5763649	0.80[EUR][1000 genomes]
rs5763670	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763671	0.83[EUR][1000 genomes]
rs5763688	0.84[EUR][1000 genomes]
rs5763775	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs5763779	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs59663694	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5997549	0.86[AFR][1000 genomes]
rs6006288	0.86[AFR][1000 genomes]
rs6006315	0.87[LWK][hapmap];1.00[YRI][hapmap]
rs713656	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs713657	0.89[CEU][hapmap]
rs7285583	0.82[EUR][1000 genomes]
rs7287570	0.81[AFR][1000 genomes]
rs73162764	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs737908	0.83[EUR][1000 genomes]
rs737911	0.96[CEU][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9306465	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs9306468	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs960987	0.87[EUR][1000 genomes]
rs9614100	0.83[AFR][1000 genomes]
rs997913	0.92[CEU][hapmap];0.83[EUR][1000 genomes]

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
rs41157	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs41157	MTMR3	cis	parietal	SCAN
rs41157	ASCC2	cis	cerebellum	SCAN
rs41157	CABP7	cis	cerebellum	SCAN
rs41157	NEFH	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	chr22:30389200-30409200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr22:30389200-30411600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr22:30389200-30411800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr22:30390200-30434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr22:30391200-30411400	Weak transcription	Small Intestine	intestine
8	chr22:30391400-30409800	Weak transcription	Fetal Heart	heart
9	chr22:30391400-30411600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr22:30391400-30433000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr22:30391600-30409800	Weak transcription	K562	blood
12	chr22:30391600-30417800	Weak transcription	Right Atrium	heart
13	chr22:30392600-30425000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr22:30393800-30424800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr22:30394600-30424600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr22:30394800-30425200	Strong transcription	Fetal Intestine Large	intestine
17	chr22:30394800-30426200	Strong transcription	Placenta	Placenta
18	chr22:30396800-30426200	Strong transcription	Primary B cells from cord blood	blood
19	chr22:30397600-30419800	Strong transcription	Dnd41	blood
20	chr22:30397800-30423800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr22:30397800-30425400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr22:30398000-30424400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr22:30398000-30426200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr22:30398200-30407400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr22:30398200-30410400	Strong transcription	HSMM	muscle
26	chr22:30398400-30425000	Strong transcription	Primary hematopoietic stem cells	blood
27	chr22:30398600-30425200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr22:30399000-30405400	Strong transcription	Fetal Intestine Small	intestine
29	chr22:30399600-30415400	Weak transcription	A549	lung
30	chr22:30399800-30422400	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr22:30400200-30406600	Strong transcription	NHEK	skin
32	chr22:30401200-30420000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr22:30401200-30423200	Strong transcription	Adipose Nuclei	Adipose
34	chr22:30401400-30411600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr22:30401600-30425200	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr22:30401800-30410200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr22:30401800-30411800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr22:30402000-30405200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
39	chr22:30402000-30422600	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr22:30402000-30422600	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr22:30402200-30425200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr22:30402400-30406800	Strong transcription	Fetal Stomach	stomach
43	chr22:30402400-30407000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr22:30402400-30407200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr22:30402400-30420800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr22:30402400-30424600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr22:30402600-30406000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr22:30402600-30406200	Strong transcription	Fetal Lung	lung
49	chr22:30402600-30406600	Strong transcription	HepG2	liver
50	chr22:30402600-30407000	Strong transcription	Left Ventricle	heart

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