Variant report

Variant	rs6006267
Chromosome Location	chr22:30216982-30216983
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:30216825-30217873	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:30207717..30211289-chr22:30214169..30217331,4	K562	blood:
2	chr22:30216228..30218392-chr22:30231989..30234163,2	K562	blood:
3	chr22:30163203..30165019-chr22:30216595..30218999,2	MCF-7	breast:
4	chr22:30168312..30170013-chr22:30216889..30218868,2	MCF-7	breast:

Variant related genes	Relation type
ASCC2	TF binding region
ENSG00000100325	Chromatin interaction
ENSG00000184076	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs131298	0.92[ASN][1000 genomes]
rs140114	0.82[GIH][hapmap]
rs140126	0.85[GIH][hapmap]
rs140139	0.82[ASN][1000 genomes]
rs140145	0.85[CEU][hapmap]
rs140149	0.85[CEU][hapmap]
rs140150	0.80[EUR][1000 genomes]
rs17711377	0.81[EUR][1000 genomes]
rs1961926	0.85[CEU][hapmap]
rs2057882	0.80[EUR][1000 genomes]
rs2074706	0.89[CEU][hapmap]
rs2074707	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2079338	0.81[EUR][1000 genomes]
rs2301402	0.85[CEU][hapmap]
rs249396	0.98[ASN][1000 genomes]
rs249397	0.97[ASN][1000 genomes]
rs249401	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36572	0.95[ASN][1000 genomes]
rs5752962	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[ASN][1000 genomes]
rs5752964	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs5752978	0.81[CEU][hapmap]
rs5763512	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs5997529	0.81[EUR][1000 genomes]
rs5997530	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs5997534	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs713656	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs713657	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs737945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs740041	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7954	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[ASN][1000 genomes]
rs9306465	0.85[CEU][hapmap]
rs9608816	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6006267	TTC28	cis	cerebellum	SCAN
rs6006267	CRYBB2	cis	parietal	SCAN
rs6006267	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs6006267	CRYBB3	cis	parietal	SCAN
rs6006267	ASCC2	cis	cerebellum	SCAN
rs6006267	CABP7	cis	cerebellum	SCAN
rs6006267	NIPSNAP1	cis	cerebellum	SCAN

Chromatin state (count:126 , 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	chr22:30182200-30217000	Strong transcription	Fetal Intestine Small	intestine
3	chr22:30182200-30222200	Strong transcription	Thymus	Thymus
4	chr22:30182800-30232200	Strong transcription	Primary T cells from cord blood	blood
5	chr22:30182800-30232200	Strong transcription	Fetal Stomach	stomach
6	chr22:30183000-30221400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr22:30183200-30230800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr22:30183400-30224000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr22:30183400-30230800	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr22:30183800-30224000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr22:30183800-30232200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr22:30184000-30222200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:30191000-30222200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr22:30193400-30217200	Strong transcription	Fetal Thymus	thymus
15	chr22:30195400-30222000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr22:30195400-30222200	Strong transcription	Primary B cells from peripheral blood	blood
17	chr22:30196000-30217000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr22:30196200-30217200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr22:30196200-30217200	Strong transcription	Duodenum Mucosa	Duodenum
20	chr22:30196200-30222200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr22:30196200-30222200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr22:30196400-30221200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr22:30197000-30222200	Strong transcription	Dnd41	blood
24	chr22:30199200-30222000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr22:30203600-30233400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr22:30204200-30217000	Weak transcription	Fetal Heart	heart
27	chr22:30205800-30217000	Strong transcription	Fetal Intestine Large	intestine
28	chr22:30205800-30222000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr22:30206000-30217000	Strong transcription	GM12878-XiMat	blood
30	chr22:30206000-30221800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr22:30206000-30221800	Strong transcription	Brain Anterior Caudate	brain
32	chr22:30208000-30217800	Strong transcription	Primary B cells from cord blood	blood
33	chr22:30208600-30217200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr22:30208800-30231000	Strong transcription	Brain Germinal Matrix	brain
35	chr22:30208800-30231200	Strong transcription	Lung	lung
36	chr22:30208800-30233400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr22:30209000-30220200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr22:30209000-30227600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr22:30209400-30217000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr22:30209800-30233600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr22:30210000-30217600	Weak transcription	Fetal Kidney	kidney
42	chr22:30210200-30217000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr22:30211000-30220200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr22:30211800-30219800	Weak transcription	Small Intestine	intestine
45	chr22:30212200-30217200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr22:30212400-30217000	Weak transcription	Fetal Lung	lung
47	chr22:30212400-30217200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr22:30212400-30218600	Strong transcription	Stomach Smooth Muscle	stomach
49	chr22:30212400-30221800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr22:30212400-30221800	Strong transcription	Brain Hippocampus Middle	brain

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