Variant report

Variant	rs3958025
Chromosome Location	chr22:30229399-30229400
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30212293..30214646-chr22:30228307..30229827,2	MCF-7	breast:
2	chr22:30228718..30231367-chr22:30232651..30236541,5	K562	blood:
3	chr22:30228546..30230856-chr22:30232707..30235317,4	MCF-7	breast:
4	chr22:30226725..30230027-chr22:30233173..30235923,3	MCF-7	breast:
5	chr22:30225765..30230715-chr22:30232604..30236000,6	K562	blood:

Variant related genes	Relation type
ENSG00000100325	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1071888	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1076137	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12168552	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs131278	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs131291	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs131294	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs131296	0.87[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[YRI][hapmap]
rs140105	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs140108	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs140135	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs140142	0.82[ASN][1000 genomes]
rs140151	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17643918	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2105870	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2349225	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs2412960	0.91[CEU][hapmap]
rs2412963	0.91[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap]
rs249400	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34862234	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35705048	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36578	1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs36580	0.82[EUR][1000 genomes]
rs36590	0.82[EUR][1000 genomes]
rs36591	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36594	0.81[EUR][1000 genomes]
rs36596	0.81[EUR][1000 genomes]
rs36598	0.81[EUR][1000 genomes]
rs36600	0.91[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs36601	0.81[EUR][1000 genomes]
rs36604	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36605	0.81[EUR][1000 genomes]
rs36606	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36607	0.81[EUR][1000 genomes]
rs3788423	0.91[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap]
rs3887275	0.91[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41162	0.82[ASW][hapmap];0.87[CEU][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap]
rs41164	0.82[CEU][hapmap];0.84[TSI][hapmap]
rs41172	0.82[ASW][hapmap];0.83[GIH][hapmap]
rs4239932	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap]
rs4820820	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4820822	0.83[EUR][1000 genomes]
rs4823055	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823063	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs4993442	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5752968	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7286070	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7292615	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs737909	0.91[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs737912	0.91[CEU][hapmap]
rs8136147	0.82[EUR][1000 genomes]
rs8139994	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8141680	0.89[YRI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9620926	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625873	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9625874	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9625878	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9625879	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3958025	TTC28	cis	cerebellum	SCAN
rs3958025	MTMR3	cis	multi-tissue	Pritchard
rs3958025	KIAA1671	cis	cerebellum	SCAN
rs3958025	NEFH	cis	cerebellum	SCAN
rs3958025	CRYBB3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30177600-30233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30182800-30232200	Strong transcription	Primary T cells from cord blood	blood
3	chr22:30182800-30232200	Strong transcription	Fetal Stomach	stomach
4	chr22:30183200-30230800	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr22:30183400-30230800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr22:30183800-30232200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr22:30203600-30233400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr22:30208800-30231000	Strong transcription	Brain Germinal Matrix	brain
9	chr22:30208800-30231200	Strong transcription	Lung	lung
10	chr22:30208800-30233400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:30209800-30233600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr22:30215000-30230800	Strong transcription	Fetal Brain Female	brain
13	chr22:30215200-30233200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr22:30218000-30230600	Strong transcription	Fetal Thymus	thymus
15	chr22:30218000-30231000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr22:30218200-30232200	Strong transcription	Fetal Intestine Small	intestine
17	chr22:30218400-30233000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr22:30218600-30230400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr22:30218600-30233400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr22:30219000-30232000	Weak transcription	Fetal Brain Male	brain
21	chr22:30219600-30233400	Weak transcription	Fetal Kidney	kidney
22	chr22:30220000-30231600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr22:30221400-30233400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr22:30221600-30233400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr22:30221800-30229400	Weak transcription	Colonic Mucosa	Colon
26	chr22:30221800-30233400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr22:30221800-30233600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr22:30222000-30232800	Weak transcription	Hela-S3	cervix
29	chr22:30222000-30233600	Weak transcription	Small Intestine	intestine
30	chr22:30223000-30230400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr22:30223000-30230600	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr22:30223000-30230600	Strong transcription	Thymus	Thymus
33	chr22:30223000-30230600	Strong transcription	Dnd41	blood
34	chr22:30223000-30230600	Strong transcription	HSMM	muscle
35	chr22:30223000-30231000	Strong transcription	Primary B cells from cord blood	blood
36	chr22:30223000-30231200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr22:30223000-30231600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr22:30223000-30232200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr22:30223000-30232200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr22:30223000-30232200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr22:30223200-30229600	Strong transcription	Rectal Smooth Muscle	rectum
42	chr22:30223200-30229800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr22:30223200-30230600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr22:30223200-30230600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr22:30223400-30231600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr22:30223600-30230600	Strong transcription	Spleen	Spleen
47	chr22:30223800-30231200	Strong transcription	Duodenum Mucosa	Duodenum
48	chr22:30224000-30230800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr22:30224200-30233200	Weak transcription	Right Atrium	heart
50	chr22:30224400-30230000	Strong transcription	Primary hematopoietic stem cells	blood

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