Variant report

Variant	rs6848779
Chromosome Location	chr4:15695497-15695498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:15688099..15691851-chr4:15693334..15695870,4	MCF-7	breast:
2	chr4:15681921..15686275-chr4:15691863..15696153,5	MCF-7	breast:
3	chr4:15690443..15693747-chr4:15694264..15697002,4	MCF-7	breast:
4	chr4:15694240..15696950-chr4:15697578..15699264,2	K562	blood:
5	chr4:15694450..15696335-chr4:15709178..15711089,2	K562	blood:
6	chr4:15681864..15684711-chr4:15693496..15696288,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237765	Chromatin interaction
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10005305	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10008878	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10015827	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10017222	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10025875	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10034315	0.89[AFR][1000 genomes]
rs10433813	0.87[ASN][1000 genomes]
rs10516289	1.00[CHB][hapmap]
rs11722300	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722854	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11723478	0.95[AFR][1000 genomes]
rs11723554	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs11729955	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11730088	0.81[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732953	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11735063	1.00[CHB][hapmap]
rs11947383	0.96[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12642407	0.96[AFR][1000 genomes]
rs12650529	0.87[AFR][1000 genomes]
rs13134177	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13150957	0.96[AFR][1000 genomes]
rs17405811	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476642	1.00[CHB][hapmap]
rs1786	0.88[ASW][hapmap];1.00[CHB][hapmap];0.98[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs28394730	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28402170	0.88[AFR][1000 genomes]
rs28447067	0.96[AFR][1000 genomes]
rs28604503	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28644177	0.96[AFR][1000 genomes]
rs28820655	0.94[AFR][1000 genomes]
rs34473224	0.96[AFR][1000 genomes]
rs34559117	0.96[AFR][1000 genomes]
rs35013326	0.94[AFR][1000 genomes]
rs35519415	0.85[EUR][1000 genomes]
rs3756246	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs3756247	1.00[CHB][hapmap]
rs3775956	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3775957	0.96[AFR][1000 genomes]
rs4267734	0.81[YRI][hapmap]
rs4301111	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs4331772	0.89[AFR][1000 genomes]
rs4346644	0.96[AFR][1000 genomes]
rs4396986	0.88[ASW][hapmap];1.00[CHB][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes]
rs4423870	0.82[ASW][hapmap];1.00[CHB][hapmap];0.89[LWK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs4484296	0.94[AFR][1000 genomes]
rs4549375	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs4554069	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4600905	0.89[AFR][1000 genomes]
rs4698116	0.89[AFR][1000 genomes]
rs6414764	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs6449150	0.85[LWK][hapmap];0.88[YRI][hapmap]
rs6449152	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6815254	0.88[ASW][hapmap];1.00[CHB][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs6815296	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816982	0.97[AFR][1000 genomes]
rs6823775	0.87[AFR][1000 genomes]
rs6824422	1.00[CHB][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs6825051	0.92[YRI][hapmap]
rs6826058	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs6827406	0.88[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6828776	0.86[AFR][1000 genomes]
rs6839654	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs6843740	0.97[AFR][1000 genomes]
rs6852735	0.86[AFR][1000 genomes]
rs6857442	0.93[AFR][1000 genomes]
rs7434484	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7667175	0.97[AFR][1000 genomes]
rs7698596	0.96[AFR][1000 genomes]
rs9994518	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6848779	FAM200B	cis	cerebellum	SCAN
rs6848779	FAM200B	cis	parietal	SCAN
rs6848779	LOC285550	cis	multi-tissue	Pritchard
rs6848779	FGFBP2	cis	lymphoblastoid	seeQTL
rs6848779	BST1	cis	multi-tissue	Pritchard

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15684000-15697000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:15684000-15704400	Weak transcription	Left Ventricle	heart
3	chr4:15684800-15704400	Weak transcription	Aorta	Aorta
4	chr4:15685000-15695800	Weak transcription	Stomach Mucosa	stomach
5	chr4:15686600-15704400	Weak transcription	Thymus	Thymus
6	chr4:15687200-15701200	Weak transcription	Fetal Intestine Small	intestine
7	chr4:15687600-15696800	Weak transcription	Fetal Stomach	stomach
8	chr4:15687600-15697000	Weak transcription	Esophagus	oesophagus
9	chr4:15688400-15697200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:15688400-15703800	Weak transcription	Fetal Kidney	kidney
11	chr4:15688600-15695600	Weak transcription	Fetal Lung	lung
12	chr4:15689600-15697200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:15690600-15697800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr4:15691000-15697000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:15691000-15698600	Weak transcription	Dnd41	blood
16	chr4:15691400-15696000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:15691400-15697200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:15691400-15698400	Weak transcription	Primary T cells from cord blood	blood
19	chr4:15691400-15698400	Weak transcription	Liver	Liver
20	chr4:15691400-15704000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:15691400-15704200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr4:15692200-15696000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:15692200-15704000	Weak transcription	Brain Germinal Matrix	brain
24	chr4:15692600-15697000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:15692800-15696800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr4:15692800-15696800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:15693200-15695600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:15693200-15695800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:15693200-15696600	Weak transcription	Hela-S3	cervix
30	chr4:15693200-15696800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr4:15693200-15696800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:15693200-15701600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr4:15693400-15696200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:15693400-15696400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:15693400-15697000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:15693400-15702800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr4:15693600-15695800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr4:15693600-15695800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:15693600-15695800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:15693600-15696000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:15693600-15698800	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr4:15693600-15701800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:15693800-15697000	Weak transcription	HSMMtube	muscle
44	chr4:15694000-15695600	Weak transcription	NHEK	skin
45	chr4:15694000-15695800	Weak transcription	HMEC	breast
46	chr4:15694000-15696800	Weak transcription	HUVEC	blood vessel
47	chr4:15694200-15697000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:15694200-15699000	Weak transcription	Primary B cells from cord blood	blood
49	chr4:15694400-15696200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:15694400-15696200	Enhancers	A549	lung

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