Variant report

Variant	rs4896680
Chromosome Location	chr6:144188547-144188548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:144181106..144183993-chr6:144186106..144189190,3	K562	blood:
2	chr6:144181106..144183993-chr6:144186106..144190381,4	K562	blood:
3	chr6:144183593..144185426-chr6:144187366..144189875,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10872563	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11155328	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810524	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1884089	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2277078	0.82[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2328508	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4140442	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4379307	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4896676	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4896678	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62427458	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918125	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6941262	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7773870	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9484817	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9496785	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3408554	chr6:144106707-144369589	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3522138	chr6:144174685-144367463	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3522139	chr6:144174685-144367463	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv830830	chr6:144177942-144380870	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4896680	STON2	trans	parietal	SCAN
rs4896680	ADAT2	cis	cerebellum	SCAN
rs4896680	C6orf103	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144166000-144188600	Strong transcription	Primary T cells from cord blood	blood
2	chr6:144172400-144189000	Weak transcription	Small Intestine	intestine
3	chr6:144178800-144203800	Weak transcription	Stomach Mucosa	stomach
4	chr6:144179800-144191200	Weak transcription	Psoas Muscle	Psoas
5	chr6:144183000-144193000	Weak transcription	Spleen	Spleen
6	chr6:144183200-144188800	Weak transcription	Colonic Mucosa	Colon
7	chr6:144183200-144189000	Weak transcription	Gastric	stomach
8	chr6:144183200-144189800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:144183200-144190400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:144183400-144189000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:144184600-144189000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:144184600-144190600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:144184800-144188800	Weak transcription	Brain Angular Gyrus	brain
14	chr6:144185600-144193000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:144185800-144190600	Weak transcription	Fetal Kidney	kidney
16	chr6:144186000-144189800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:144186000-144192400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:144186000-144192800	Weak transcription	HSMMtube	muscle
19	chr6:144186000-144223000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr6:144186200-144188800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:144186200-144193200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr6:144186600-144188800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:144186600-144188800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:144186600-144189400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:144186600-144193000	Weak transcription	Osteobl	bone
26	chr6:144186600-144193200	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr6:144186800-144188600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:144186800-144188800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:144186800-144189000	Weak transcription	NHLF	lung
30	chr6:144186800-144189200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:144186800-144189400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:144186800-144190600	Weak transcription	Brain Germinal Matrix	brain
33	chr6:144186800-144193000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr6:144187000-144188800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:144187000-144189200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:144187000-144189200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:144187000-144189200	Weak transcription	HSMM	muscle
38	chr6:144187000-144189200	Weak transcription	NH-A	brain
39	chr6:144187000-144192000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:144187000-144193200	Weak transcription	NHEK	skin
41	chr6:144187000-144193800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:144187200-144191600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:144187400-144188800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:144187400-144188800	Weak transcription	Dnd41	blood
45	chr6:144187400-144189000	Weak transcription	HMEC	breast
46	chr6:144187400-144189200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr6:144187400-144189200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:144187400-144189200	Weak transcription	Liver	Liver
49	chr6:144187400-144189200	Weak transcription	Fetal Intestine Large	intestine
50	chr6:144187600-144188800	Weak transcription	Brain Anterior Caudate	brain

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