Variant report

Variant	rs6901411
Chromosome Location	chr6:33633527-33633528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33625658..33632208-chr6:33632440..33635133,7	MCF-7	breast:
2	chr6:33632139..33634646-chr6:33635663..33639290,5	K562	blood:
3	chr6:33623872..33628631-chr6:33630927..33635524,5	K562	blood:
4	chr6:33632367..33634802-chr6:33639776..33642394,2	K562	blood:
5	chr6:33632939..33634646-chr6:33637340..33638930,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12662536	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1408711	0.81[JPT][hapmap]
rs1570759	0.83[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2229634	0.81[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2274198	0.81[EUR][1000 genomes]
rs2296336	0.81[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2296337	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2296343	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6908236	0.85[CHD][hapmap]
rs9368771	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9394158	0.81[JPT][hapmap]

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	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv470811	chr6:33622933-33647651	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv602838	chr6:33624733-33650743	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv885771	chr6:33626717-33660143	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6901411	STK38	cis	parietal	SCAN
rs6901411	RPL10A	cis	parietal	SCAN
rs6901411	C6orf126	cis	cerebellum	SCAN
rs6901411	SPDEF	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33602400-33636400	Weak transcription	HSMMtube	muscle
2	chr6:33603400-33640400	Weak transcription	HUVEC	blood vessel
3	chr6:33603400-33641200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:33605200-33636400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:33606800-33646600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:33608200-33640800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:33611400-33643400	Weak transcription	Left Ventricle	heart
8	chr6:33613000-33659400	Strong transcription	Fetal Intestine Small	intestine
9	chr6:33613200-33660400	Strong transcription	Thymus	Thymus
10	chr6:33613400-33635400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:33613600-33635000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr6:33614400-33636200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr6:33615000-33660800	Strong transcription	Fetal Intestine Large	intestine
14	chr6:33619600-33660800	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr6:33621000-33659400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr6:33621200-33636200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:33621200-33636400	Strong transcription	Primary T cells from cord blood	blood
18	chr6:33621200-33636400	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:33621400-33635800	Strong transcription	Colonic Mucosa	Colon
20	chr6:33621400-33636400	Strong transcription	Lung	lung
21	chr6:33621400-33643400	Strong transcription	Spleen	Spleen
22	chr6:33621400-33662200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:33621400-33672600	Strong transcription	Dnd41	blood
24	chr6:33622000-33660000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:33622400-33644400	Strong transcription	Gastric	stomach
26	chr6:33623000-33635200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:33623200-33634800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:33623200-33635600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:33623200-33636200	Strong transcription	HMEC	breast
30	chr6:33623200-33649000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr6:33623400-33641000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:33623400-33644000	Strong transcription	Fetal Stomach	stomach
33	chr6:33624200-33636200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:33624200-33639200	Strong transcription	NHLF	lung
35	chr6:33624600-33635800	Weak transcription	HepG2	liver
36	chr6:33624600-33664800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr6:33624800-33639400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:33625200-33634800	Weak transcription	Placenta	Placenta
39	chr6:33625200-33645200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:33625600-33636200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr6:33625800-33635600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:33626000-33635200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr6:33626000-33638600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:33626400-33634000	Weak transcription	HSMM	muscle
45	chr6:33626600-33636000	Weak transcription	K562	blood
46	chr6:33626600-33638800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:33626800-33634200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr6:33627000-33635400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:33627200-33636000	Weak transcription	Fetal Lung	lung
50	chr6:33627400-33635200	Weak transcription	A549	lung

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