Variant report

Variant	rs6675292
Chromosome Location	chr1:197747067-197747068
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197743225..197745756-chr1:197745981..197751358,8	MCF-7	breast:
2	chr1:197740677..197742202-chr1:197746593..197748799,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213047	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10754228	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10922260	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10922289	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10922291	0.97[ASN][1000 genomes]
rs12066841	0.86[ASN][1000 genomes]
rs12081207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564235	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2111930	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs4268380	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4274099	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4915561	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4915564	0.98[ASN][1000 genomes]
rs4915567	0.82[AFR][1000 genomes]
rs55995691	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6428416	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6667560	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6691216	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs7516334	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7516481	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7533766	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427908	chr1:197611569-197767362	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6675292	DENND1B	cis	cerebellum	SCAN

Chromatin state (count:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197744600-197751200	Weak transcription	Small Intestine	intestine
2	chr1:197745200-197748200	Enhancers	Primary B cells from cord blood	blood
3	chr1:197745200-197748400	Enhancers	Dnd41	blood
4	chr1:197745200-197748800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:197745200-197752800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:197745200-197756800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:197745400-197747600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr1:197745400-197749000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:197745400-197751200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:197745400-197752000	Weak transcription	Esophagus	oesophagus
11	chr1:197745600-197747400	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr1:197745600-197747600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:197745600-197748200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:197745600-197748200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr1:197745600-197748200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:197745600-197748200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr1:197745600-197748600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr1:197745600-197751000	Weak transcription	NHLF	lung
19	chr1:197745800-197747400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:197745800-197751000	Weak transcription	Stomach Mucosa	stomach
21	chr1:197745800-197751400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:197746000-197747200	Weak transcription	Thymus	Thymus
23	chr1:197746000-197747400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:197746000-197748200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:197746000-197748400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr1:197746000-197751000	Weak transcription	Fetal Intestine Large	intestine
27	chr1:197746000-197751200	Weak transcription	Fetal Intestine Small	intestine
28	chr1:197746000-197751200	Weak transcription	Hela-S3	cervix
29	chr1:197746200-197747200	Weak transcription	K562	blood
30	chr1:197746200-197747400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:197746200-197747400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:197746200-197747600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:197746200-197747800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:197746200-197750600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:197746200-197750600	Weak transcription	NHEK	skin
36	chr1:197746200-197751000	Weak transcription	NHDF-Ad	bronchial
37	chr1:197746200-197751000	Weak transcription	Osteobl	bone
38	chr1:197746200-197751200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:197746200-197751200	Weak transcription	HMEC	breast
40	chr1:197746400-197747400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr1:197746400-197747400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:197746400-197748000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:197746400-197751000	Weak transcription	Colonic Mucosa	Colon
44	chr1:197746400-197751200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:197746600-197747600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr1:197746600-197747600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr1:197746600-197747600	Enhancers	GM12878-XiMat	blood
48	chr1:197746600-197751200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:197746800-197747200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:197746800-197747200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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