Variant report

Variant	rs6469842
Chromosome Location	chr8:120777991-120777992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 137 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10086597	1.00[ASN][1000 genomes]
rs10088028	1.00[ASN][1000 genomes]
rs10089043	1.00[ASN][1000 genomes]
rs10089416	1.00[CEU][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10090726	1.00[ASN][1000 genomes]
rs10093746	1.00[ASN][1000 genomes]
rs10095185	1.00[ASN][1000 genomes]
rs10095406	1.00[ASN][1000 genomes]
rs10095508	1.00[ASN][1000 genomes]
rs10095955	1.00[ASN][1000 genomes]
rs10097203	1.00[ASN][1000 genomes]
rs10097757	1.00[ASN][1000 genomes]
rs10098362	1.00[ASN][1000 genomes]
rs10099163	1.00[ASN][1000 genomes]
rs10101222	1.00[ASN][1000 genomes]
rs10101391	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10101983	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10102102	1.00[ASN][1000 genomes]
rs10102508	1.00[ASN][1000 genomes]
rs10104449	1.00[ASN][1000 genomes]
rs10105858	1.00[ASN][1000 genomes]
rs10106425	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10108101	0.80[ASW][hapmap]
rs10109920	1.00[ASN][1000 genomes]
rs10109941	1.00[ASN][1000 genomes]
rs10110853	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10505373	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11552092	0.85[EUR][1000 genomes]
rs12334414	1.00[ASN][1000 genomes]
rs12334539	1.00[ASN][1000 genomes]
rs12334592	1.00[ASN][1000 genomes]
rs12386813	1.00[ASN][1000 genomes]
rs13439791	1.00[ASN][1000 genomes]
rs1355174	0.87[ASW][hapmap]
rs1433949	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16892875	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893011	1.00[ASN][1000 genomes]
rs16893021	1.00[ASN][1000 genomes]
rs16893034	1.00[ASN][1000 genomes]
rs16893117	1.00[CEU][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes]
rs16893176	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs16893201	0.83[EUR][1000 genomes]
rs2139432	1.00[ASN][1000 genomes]
rs2164021	1.00[ASN][1000 genomes]
rs28393075	1.00[ASN][1000 genomes]
rs28436011	1.00[ASN][1000 genomes]
rs28447970	1.00[ASN][1000 genomes]
rs28449953	1.00[ASN][1000 genomes]
rs28502370	1.00[ASN][1000 genomes]
rs28517862	1.00[ASN][1000 genomes]
rs28529634	1.00[ASN][1000 genomes]
rs28570063	1.00[ASN][1000 genomes]
rs28575743	1.00[ASN][1000 genomes]
rs28579855	1.00[ASN][1000 genomes]
rs28589493	1.00[ASN][1000 genomes]
rs28636993	1.00[ASN][1000 genomes]
rs28637899	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28673002	1.00[ASN][1000 genomes]
rs28673290	1.00[ASN][1000 genomes]
rs28678910	1.00[ASN][1000 genomes]
rs28684724	1.00[ASN][1000 genomes]
rs28701610	1.00[ASN][1000 genomes]
rs28723382	1.00[ASN][1000 genomes]
rs28735236	1.00[ASN][1000 genomes]
rs28852781	1.00[ASN][1000 genomes]
rs4871029	1.00[ASN][1000 genomes]
rs4871774	1.00[ASN][1000 genomes]
rs4871792	1.00[ASN][1000 genomes]
rs55834530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56116632	0.81[EUR][1000 genomes]
rs56168312	0.81[EUR][1000 genomes]
rs56285268	0.81[EUR][1000 genomes]
rs56369293	0.81[EUR][1000 genomes]
rs56712359	0.81[EUR][1000 genomes]
rs57094219	0.81[EUR][1000 genomes]
rs57423283	0.87[EUR][1000 genomes]
rs60576513	0.81[EUR][1000 genomes]
rs60762762	0.81[EUR][1000 genomes]
rs61585800	0.81[EUR][1000 genomes]
rs6469843	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469845	0.87[ASW][hapmap]
rs6469847	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6469848	0.89[EUR][1000 genomes]
rs6980897	1.00[ASN][1000 genomes]
rs6981151	1.00[ASN][1000 genomes]
rs6984913	1.00[ASN][1000 genomes]
rs6986364	1.00[ASN][1000 genomes]
rs6989251	0.81[EUR][1000 genomes]
rs6989284	1.00[ASN][1000 genomes]
rs6989323	1.00[ASN][1000 genomes]
rs6990166	1.00[ASN][1000 genomes]
rs6994085	0.87[ASW][hapmap]
rs6994297	0.89[EUR][1000 genomes]
rs6995449	0.81[EUR][1000 genomes]
rs6996373	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6998771	1.00[ASN][1000 genomes]
rs7002501	0.87[ASW][hapmap]
rs7006490	1.00[ASN][1000 genomes]
rs7009770	1.00[ASN][1000 genomes]
rs7010474	1.00[ASN][1000 genomes]
rs7010646	1.00[ASN][1000 genomes]
rs7010729	1.00[ASN][1000 genomes]
rs7010887	1.00[ASN][1000 genomes]
rs72673603	1.00[ASN][1000 genomes]
rs72673616	1.00[ASN][1000 genomes]
rs72673617	1.00[ASN][1000 genomes]
rs72673639	1.00[ASN][1000 genomes]
rs72673643	1.00[ASN][1000 genomes]
rs72690149	1.00[ASN][1000 genomes]
rs73702609	0.89[EUR][1000 genomes]
rs73702610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73702612	0.89[EUR][1000 genomes]
rs73713100	0.81[EUR][1000 genomes]
rs73713102	0.81[EUR][1000 genomes]
rs7827756	0.81[EUR][1000 genomes]
rs7831321	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7833407	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7833422	1.00[ASN][1000 genomes]
rs7835482	1.00[CEU][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes]
rs7839002	0.80[CEU][hapmap]
rs7839841	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7843034	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7843631	1.00[ASN][1000 genomes]
rs9297606	0.87[ASW][hapmap]
rs956748	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs956749	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9656932	1.00[ASN][1000 genomes]
rs9693192	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9987078	1.00[ASN][1000 genomes]
rs9987272	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534028	chr8:120348940-120906079	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv949368	chr8:120568034-121019872	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1021071	chr8:120589963-120968317	Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv465789	chr8:120636850-120994394	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv612111	chr8:120636850-120994394	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv427826	chr8:120642181-120953395	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6469842	TAF2	cis	Thyroid	GTEx
rs6469842	TAF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120719400-120779600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:120734600-120779600	Weak transcription	Gastric	stomach
3	chr8:120736600-120779600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr8:120736600-120779800	Weak transcription	Aorta	Aorta
5	chr8:120736600-120779800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr8:120737600-120779000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr8:120737800-120779600	Weak transcription	Lung	lung
8	chr8:120741000-120779600	Weak transcription	Pancreas	Pancrea
9	chr8:120742200-120780800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr8:120742400-120778400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr8:120742400-120779400	Weak transcription	Esophagus	oesophagus
12	chr8:120742400-120782600	Weak transcription	Fetal Heart	heart
13	chr8:120742600-120812800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr8:120744000-120814600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr8:120744400-120779400	Weak transcription	Spleen	Spleen
16	chr8:120744400-120824400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr8:120745400-120779000	Weak transcription	Colon Smooth Muscle	Colon
18	chr8:120748600-120778800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr8:120750800-120779600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr8:120750800-120780200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr8:120752600-120778600	Weak transcription	Thymus	Thymus
22	chr8:120754600-120779400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr8:120755600-120779400	Weak transcription	Stomach Mucosa	stomach
24	chr8:120757400-120779600	Weak transcription	Brain Angular Gyrus	brain
25	chr8:120757400-120779600	Weak transcription	Brain Anterior Caudate	brain
26	chr8:120757400-120780000	Weak transcription	Ovary	ovary
27	chr8:120757400-120780400	Weak transcription	Fetal Kidney	kidney
28	chr8:120759200-120790600	Weak transcription	Fetal Brain Male	brain
29	chr8:120760200-120779800	Weak transcription	Brain Substantia Nigra	brain
30	chr8:120760600-120804600	Weak transcription	Psoas Muscle	Psoas
31	chr8:120761200-120779600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr8:120761600-120779800	Weak transcription	NHEK	skin
33	chr8:120761600-120800800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr8:120766600-120784000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr8:120767200-120807400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr8:120767800-120778600	Weak transcription	Fetal Stomach	stomach
37	chr8:120767800-120778800	Weak transcription	Fetal Intestine Small	intestine
38	chr8:120768400-120778400	Weak transcription	Fetal Muscle Leg	muscle
39	chr8:120768600-120786800	Weak transcription	Small Intestine	intestine
40	chr8:120769400-120778200	Weak transcription	A549	lung
41	chr8:120769400-120779200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr8:120769400-120779600	Weak transcription	Brain Hippocampus Middle	brain
43	chr8:120769400-120779600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr8:120770000-120779600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr8:120770000-120779600	Weak transcription	Brain Germinal Matrix	brain
46	chr8:120770000-120779600	Weak transcription	Colonic Mucosa	Colon
47	chr8:120770400-120779800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr8:120770400-120787400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr8:120771000-120789000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr8:120772200-120779800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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