Variant report

Variant	rs6006098
Chromosome Location	chr22:29734797-29734798
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	chr22:29733917..29736788-chr22:29738344..29740260,2	K562	blood:
2	chr22:29734080..29735582-chr22:29739639..29742081,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11090564	0.87[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs131180	0.83[ASN][1000 genomes]
rs131182	0.80[ASN][1000 genomes]
rs131189	0.80[ASN][1000 genomes]
rs140062	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs140063	0.83[ASN][1000 genomes]
rs140066	0.84[ASN][1000 genomes]
rs174759	0.87[ASN][1000 genomes]
rs174761	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs174762	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap]
rs174764	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs174765	0.87[ASN][1000 genomes]
rs174766	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs174769	0.84[ASN][1000 genomes]
rs174770	0.88[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs174771	0.84[ASN][1000 genomes]
rs2071578	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2072051	0.88[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs2267132	0.82[CHB][hapmap]
rs2267133	0.88[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs2283849	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2283850	0.88[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2301290	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2301585	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2857462	0.83[ASN][1000 genomes]
rs2857466	0.83[JPT][hapmap]
rs28755	0.86[ASN][1000 genomes]
rs3788410	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs3788411	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4820803	1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap]
rs4820804	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap]
rs5752903	0.88[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs5763138	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs5763139	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs5763178	0.84[ASN][1000 genomes]
rs6006090	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs715494	0.88[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs879580	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9537	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs98069	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6006098	KREMEN1	cis	cerebellum	SCAN
rs6006098	RNF185	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29707400-29740000	Weak transcription	Hela-S3	cervix
2	chr22:29720600-29740000	Weak transcription	Fetal Brain Male	brain
3	chr22:29721400-29738200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr22:29721400-29746800	Strong transcription	Fetal Intestine Small	intestine
5	chr22:29721800-29739600	Strong transcription	Colonic Mucosa	Colon
6	chr22:29721800-29756800	Strong transcription	Primary T cells from cord blood	blood
7	chr22:29722000-29739200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr22:29722000-29739800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr22:29722000-29747000	Strong transcription	Duodenum Mucosa	Duodenum
10	chr22:29722000-29759200	Strong transcription	Dnd41	blood
11	chr22:29722000-29759800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr22:29722200-29737000	Strong transcription	Pancreas	Pancrea
13	chr22:29722200-29738000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr22:29722200-29738000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr22:29722200-29739400	Strong transcription	Fetal Brain Female	brain
16	chr22:29722200-29741000	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr22:29722200-29755800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr22:29722200-29756400	Strong transcription	Thymus	Thymus
19	chr22:29722200-29756600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr22:29722200-29759800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr22:29722400-29735000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr22:29722400-29736600	Weak transcription	Fetal Heart	heart
23	chr22:29722400-29739400	Strong transcription	Brain Germinal Matrix	brain
24	chr22:29722400-29740400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr22:29722400-29740400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
26	chr22:29722400-29756800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr22:29722400-29758400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr22:29722600-29738000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr22:29722600-29738400	Strong transcription	Aorta	Aorta
30	chr22:29722600-29739800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr22:29722600-29751200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr22:29722600-29753200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr22:29722600-29755400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr22:29722600-29756000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr22:29722600-29757200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr22:29722600-29758000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr22:29722600-29758800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr22:29723000-29739400	Strong transcription	Fetal Thymus	thymus
39	chr22:29723000-29758800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr22:29723000-29765000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr22:29724000-29739800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr22:29725400-29756200	Strong transcription	Primary B cells from cord blood	blood
43	chr22:29727200-29736800	Strong transcription	Right Ventricle	heart
44	chr22:29727400-29738800	Strong transcription	Colon Smooth Muscle	Colon
45	chr22:29727400-29738800	Strong transcription	Lung	lung
46	chr22:29727400-29739800	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr22:29727400-29739800	Strong transcription	Ovary	ovary
48	chr22:29727400-29741000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr22:29727400-29756200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr22:29727600-29739200	Strong transcription	Stomach Smooth Muscle	stomach

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