Variant report

Variant	rs13207848
Chromosome Location	chr6:34994686-34994687
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34994556..34998578-chr6:34998827..35004744,6	K562	blood:
2	chr6:34986567..34989328-chr6:34993280..34995092,2	K562	blood:
3	chr6:34984374..34990603-chr6:34991816..34996687,6	K562	blood:
4	chr6:34989723..34992184-chr6:34994409..34996173,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187762	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1051115	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1093986	0.88[EUR][1000 genomes]
rs11552398	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs11961798	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11964930	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13196367	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13196771	0.81[EUR][1000 genomes]
rs13196785	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs13199238	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13203612	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs13205210	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs13206654	0.83[EUR][1000 genomes]
rs13208078	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs13211490	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13214114	0.88[EUR][1000 genomes]
rs13215208	0.80[ASN][1000 genomes]
rs13216424	0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs13217848	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13219307	0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs16871749	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs16871809	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs16871814	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs16896559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1747516	0.88[EUR][1000 genomes]
rs1747517	0.85[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs17610836	0.85[EUR][1000 genomes]
rs2177380	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[ASN][1000 genomes]
rs2234044	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2234045	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2296361	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2296362	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2395608	0.82[EUR][1000 genomes]
rs2395610	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2494098	0.81[EUR][1000 genomes]
rs2762336	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34069418	0.85[ASN][1000 genomes]
rs34103100	0.83[EUR][1000 genomes]
rs34208177	0.88[EUR][1000 genomes]
rs34250961	0.83[EUR][1000 genomes]
rs34715060	0.81[EUR][1000 genomes]
rs34930033	0.84[EUR][1000 genomes]
rs35095464	0.88[EUR][1000 genomes]
rs35576171	0.91[ASN][1000 genomes]
rs35693439	0.80[EUR][1000 genomes]
rs3734261	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs3734266	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs3756856	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs41270044	0.89[ASN][1000 genomes]
rs41270050	0.86[EUR][1000 genomes]
rs4628094	0.83[EUR][1000 genomes]
rs4646933	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs57111149	0.88[EUR][1000 genomes]
rs57844307	0.92[ASN][1000 genomes]
rs6457797	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs66579470	0.83[EUR][1000 genomes]
rs66753029	0.82[EUR][1000 genomes]
rs67167177	0.88[EUR][1000 genomes]
rs67388064	0.97[ASN][1000 genomes]
rs67638810	0.83[EUR][1000 genomes]
rs67941146	0.88[EUR][1000 genomes]
rs6899618	0.88[EUR][1000 genomes]
rs6906666	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs6913286	0.88[EUR][1000 genomes]
rs6913975	0.88[EUR][1000 genomes]
rs6915649	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6925175	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6926532	0.83[EUR][1000 genomes]
rs6936337	0.88[EUR][1000 genomes]
rs6942104	0.88[EUR][1000 genomes]
rs728238	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs72896231	0.94[ASN][1000 genomes]
rs72896254	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72897804	0.83[EUR][1000 genomes]
rs763155	1.00[GIH][hapmap]
rs7739385	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7743949	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7761391	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7766770	0.83[EUR][1000 genomes]
rs7767073	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs820061	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs820062	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs820063	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs820065	0.85[CEU][hapmap];0.92[CHB][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs820066	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs820067	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs820069	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs820072	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs820077	0.84[CHB][hapmap]
rs820095	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs820099	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs820100	0.90[EUR][1000 genomes]
rs820101	0.85[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs820103	0.85[CEU][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs9394282	1.00[GIH][hapmap]
rs9462027	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs9462054	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13207848	DEF6	cis	multi-tissue	Pritchard
rs13207848	TCP11	cis	multi-tissue	Pritchard
rs13207848	TCP11	cis	lymphoblastoid	seeQTL
rs13207848	BRPF3	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34939400-35016000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:34963600-35006600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:34979800-35002000	Weak transcription	GM12878-XiMat	blood
4	chr6:34986200-34996400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:34986200-35015000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr6:34986400-35011800	Weak transcription	Dnd41	blood
7	chr6:34986800-35014800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:34987000-35009000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:34987000-35015800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:34987400-34998600	Weak transcription	Primary B cells from cord blood	blood
11	chr6:34987400-34999200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr6:34987400-34999600	Weak transcription	Fetal Kidney	kidney
13	chr6:34987400-35015800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:34988400-34995000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr6:34988400-34995600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr6:34988600-34999200	Enhancers	Brain Anterior Caudate	brain
17	chr6:34989000-35002800	Weak transcription	Fetal Thymus	thymus
18	chr6:34989200-34996000	Weak transcription	Pancreas	Pancrea
19	chr6:34989400-34996800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:34989400-35002200	Weak transcription	Thymus	Thymus
21	chr6:34990000-34995200	Enhancers	Colon Smooth Muscle	Colon
22	chr6:34990000-34998400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:34990200-34995600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr6:34990800-34994800	Weak transcription	Primary T cells from cord blood	blood
25	chr6:34990800-34995000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr6:34990800-34996800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:34990800-34997600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:34990800-35002800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:34991000-34995000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:34991200-34995400	Weak transcription	Gastric	stomach
31	chr6:34991200-34995800	Enhancers	Adipose Nuclei	Adipose
32	chr6:34991400-34994800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr6:34991400-34995000	Enhancers	Left Ventricle	heart
34	chr6:34991800-34994800	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr6:34991800-34995000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:34991800-34995000	Enhancers	NHDF-Ad	bronchial
37	chr6:34991800-34995200	Enhancers	HMEC	breast
38	chr6:34991800-34996000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:34992000-34995000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:34992000-34995000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:34992000-34995000	Enhancers	NHEK	skin
42	chr6:34992000-34995200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:34992200-34995000	Enhancers	Osteobl	bone
44	chr6:34992200-34995200	Enhancers	NH-A	brain
45	chr6:34992400-34995000	Enhancers	Colonic Mucosa	Colon
46	chr6:34992400-34995000	Enhancers	Spleen	Spleen
47	chr6:34992600-34995400	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr6:34992800-34995000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:34992800-34995000	Enhancers	Hela-S3	cervix
50	chr6:34992800-34995000	Weak transcription	HepG2	liver

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