Variant report

Variant	rs105311
Chromosome Location	chr22:30137262-30137263
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	chr22:30135111..30137455-chr22:30141470..30144208,2	K562	blood:
2	chr22:30136102..30138464-chr22:30143800..30146252,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs131259	0.87[AMR][1000 genomes]
rs131260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs131261	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs131262	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs131263	0.99[ASN][1000 genomes]
rs131264	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs131265	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs131266	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs131267	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs131268	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs131270	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs131271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131272	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131273	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131274	0.94[ASN][1000 genomes]
rs131275	0.80[AMR][1000 genomes]
rs131277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131281	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131284	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs131285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131286	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131287	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs131301	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[EUR][1000 genomes]
rs140094	0.81[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs140095	0.97[ASN][1000 genomes]
rs140096	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs140097	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs140099	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs140100	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140101	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140102	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140103	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs140104	0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs140106	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs140107	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140110	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140111	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs140113	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs140114	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140117	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs140118	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs140119	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140120	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140121	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140122	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140123	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140124	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs140126	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140127	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140128	0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140129	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140131	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140145	0.87[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap]
rs140149	0.87[CHB][hapmap];0.81[GIH][hapmap]
rs2074706	0.87[CHB][hapmap]
rs2074707	0.87[CHB][hapmap]
rs249398	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[EUR][1000 genomes]
rs36574	0.85[EUR][1000 genomes]
rs36576	0.81[CEU][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs5752961	0.81[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5752964	0.87[CHB][hapmap];0.81[GIH][hapmap]
rs5763512	0.87[CHB][hapmap]
rs5997530	0.87[CHB][hapmap]
rs713656	0.87[CHB][hapmap]
rs713657	0.87[CHB][hapmap]
rs715595	0.96[GIH][hapmap]
rs737932	0.96[GIH][hapmap]
rs740041	0.87[CHB][hapmap]
rs81800	0.81[CEU][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs9306465	0.87[CHB][hapmap]
rs9614055	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv914964	chr22:30081715-30150549	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv515720	chr22:30081715-30163526	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv914966	chr22:30088442-30138548	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1065072	chr22:30102176-30155245	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs105311	TTC28AS	cis	cerebellum	SCAN
rs105311	CABP7	cis	cerebellum	SCAN
rs105311	CRYBB3	cis	parietal	SCAN
rs105311	NIPSNAP1	cis	cerebellum	SCAN
rs105311	TTC28	cis	cerebellum	SCAN
rs105311	NIPSNAP1	cis	parietal	SCAN
rs105311	KIAA1671	cis	cerebellum	SCAN
rs105311	NEFH	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30123200-30137600	Weak transcription	Osteobl	bone
2	chr22:30123200-30142800	Weak transcription	Brain Substantia Nigra	brain
3	chr22:30123600-30146800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:30123600-30147000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr22:30125400-30146200	Weak transcription	NHLF	lung
6	chr22:30126000-30144600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr22:30126600-30145200	Strong transcription	Primary T cells from cord blood	blood
8	chr22:30127600-30140600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr22:30129000-30139200	Strong transcription	Stomach Smooth Muscle	stomach
10	chr22:30129400-30139000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr22:30129400-30144600	Strong transcription	Liver	Liver
12	chr22:30129800-30138600	Strong transcription	Left Ventricle	heart
13	chr22:30129800-30141000	Strong transcription	Fetal Stomach	stomach
14	chr22:30130000-30141000	Weak transcription	Colon Smooth Muscle	Colon
15	chr22:30130200-30150200	Weak transcription	A549	lung
16	chr22:30130400-30150600	Strong transcription	Fetal Intestine Small	intestine
17	chr22:30130600-30140200	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr22:30130600-30149800	Weak transcription	Psoas Muscle	Psoas
19	chr22:30130800-30138000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr22:30130800-30138800	Strong transcription	Spleen	Spleen
21	chr22:30130800-30139200	Weak transcription	NH-A	brain
22	chr22:30131000-30138800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr22:30131000-30145800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr22:30131200-30139800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr22:30131400-30148600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr22:30131600-30142200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr22:30131600-30144800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr22:30131600-30145600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr22:30131600-30162000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr22:30131800-30138800	Strong transcription	Brain Germinal Matrix	brain
31	chr22:30131800-30138800	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr22:30131800-30147200	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr22:30132800-30138800	Strong transcription	Fetal Intestine Large	intestine
34	chr22:30133000-30140000	Strong transcription	Fetal Brain Female	brain
35	chr22:30133200-30137600	Strong transcription	Thymus	Thymus
36	chr22:30133200-30139000	Strong transcription	Lung	lung
37	chr22:30133200-30139200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr22:30133200-30144600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr22:30133400-30137400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr22:30133400-30137400	Strong transcription	Fetal Thymus	thymus
41	chr22:30133400-30137600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr22:30133400-30138400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr22:30133400-30138600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr22:30133400-30138600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr22:30133400-30138600	Strong transcription	Brain Hippocampus Middle	brain
46	chr22:30133400-30138800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr22:30133400-30138800	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr22:30133400-30138800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr22:30133400-30140800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr22:30133400-30144600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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