Variant report

Variant	rs6499249
Chromosome Location	chr16:69782677-69782678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69360082..69362485-chr16:69781054..69783999,2	K562	blood:
2	chr16:69741256..69744048-chr16:69782349..69784566,2	MCF-7	breast:
3	chr16:69756628..69762611-chr16:69781362..69792848,24	MCF-7	breast:
4	chr16:69757842..69766785-chr16:69777221..69785696,15	K562	blood:

Variant related genes	Relation type
ENSG00000181019	Chromatin interaction
ENSG00000238683	Chromatin interaction
ENSG00000262136	Chromatin interaction
ENSG00000261602	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10400956	0.88[ASN][1000 genomes]
rs10517	0.86[CHD][hapmap];0.83[GIH][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap]
rs11075736	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1139177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11862697	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12019048	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs12149920	0.85[ASN][1000 genomes]
rs1318651	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13329844	0.81[CHD][hapmap]
rs16958997	0.84[CHD][hapmap];0.83[GIH][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs16959059	0.88[CEU][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs16959266	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2088747	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2291960	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2304526	0.84[CHD][hapmap];0.83[GIH][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs2917665	0.81[EUR][1000 genomes]
rs2917667	0.88[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2917669	0.88[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2917673	0.83[EUR][1000 genomes]
rs2917674	0.82[EUR][1000 genomes]
rs2917681	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2917682	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2917683	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2937120	0.83[ASN][1000 genomes]
rs2937123	0.83[ASN][1000 genomes]
rs2937126	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs2937127	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2965753	0.88[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs2965756	0.83[ASN][1000 genomes]
rs2965759	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2965760	0.82[ASN][1000 genomes]
rs2965761	0.82[ASN][1000 genomes]
rs2965762	0.84[ASN][1000 genomes]
rs2965763	0.84[ASN][1000 genomes]
rs2965764	0.84[ASN][1000 genomes]
rs3785075	1.00[YRI][hapmap]
rs3790084	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3790087	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3790088	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3826154	0.84[CHD][hapmap];0.86[GIH][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs4247107	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4247109	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4442796	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4608327	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4619391	0.86[ASN][1000 genomes]
rs4985527	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs4985529	0.86[ASN][1000 genomes]
rs4985531	0.87[ASN][1000 genomes]
rs61090597	0.81[ASN][1000 genomes]
rs6499248	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6499250	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6499259	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs689452	0.88[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs689456	0.83[EUR][1000 genomes]
rs7188187	0.84[ASN][1000 genomes]
rs7204615	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7359387	0.84[CHD][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs8050369	0.86[ASN][1000 genomes]
rs8052459	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8057938	0.88[CEU][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8058594	0.83[ASN][1000 genomes]
rs8062076	0.88[ASN][1000 genomes]
rs9888980	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs9888981	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9888993	0.83[GIH][hapmap];0.88[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs9922223	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9924953	0.86[GIH][hapmap];0.83[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs9925037	0.84[CHD][hapmap];0.88[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs9927105	0.88[ASN][1000 genomes]
rs9932486	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9934681	0.88[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs9936464	0.84[CHD][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs9937018	1.00[YRI][hapmap]
rs9940008	0.88[CEU][hapmap]

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	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv524364	chr16:69745145-69803443	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6499249	TMCO7	cis	cerebellum	SCAN
rs6499249	FUK	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69761800-69787400	Weak transcription	Right Atrium	heart
2	chr16:69770400-69788000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:69771800-69786400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr16:69772600-69786400	Strong transcription	Fetal Stomach	stomach
5	chr16:69772800-69786400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr16:69773000-69783000	Strong transcription	HepG2	liver
7	chr16:69773000-69783400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
8	chr16:69773000-69783400	Strong transcription	Primary T cells from cord blood	blood
9	chr16:69773000-69785600	Strong transcription	Stomach Smooth Muscle	stomach
10	chr16:69773000-69786000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr16:69773000-69786000	Strong transcription	Thymus	Thymus
12	chr16:69773000-69786200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr16:69773000-69786200	Strong transcription	Fetal Brain Female	brain
14	chr16:69773000-69786200	Strong transcription	Dnd41	blood
15	chr16:69773000-69786400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr16:69773000-69786600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr16:69773000-69786600	Strong transcription	Fetal Thymus	thymus
18	chr16:69773000-69786800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr16:69773000-69787000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr16:69773000-69787000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr16:69773000-69787000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr16:69773000-69787000	Strong transcription	Fetal Muscle Leg	muscle
23	chr16:69773000-69787200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr16:69773200-69785200	Strong transcription	Spleen	Spleen
25	chr16:69773200-69785600	Strong transcription	Brain Germinal Matrix	brain
26	chr16:69773200-69785800	Strong transcription	Pancreas	Pancrea
27	chr16:69773200-69786000	Strong transcription	GM12878-XiMat	blood
28	chr16:69773200-69786800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr16:69773400-69785800	Strong transcription	Fetal Lung	lung
30	chr16:69773400-69786200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr16:69773600-69786400	Strong transcription	K562	blood
32	chr16:69773800-69785800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr16:69773800-69786000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr16:69773800-69786200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr16:69773800-69786200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr16:69773800-69786200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr16:69773800-69786400	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr16:69773800-69786600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr16:69773800-69786600	Strong transcription	HSMM	muscle
40	chr16:69773800-69786800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr16:69774000-69783400	Strong transcription	Rectal Smooth Muscle	rectum
42	chr16:69774000-69785800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr16:69774000-69786200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr16:69774000-69786200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr16:69774000-69786200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr16:69774000-69786200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr16:69774000-69786600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr16:69774200-69783600	Strong transcription	NHLF	lung
49	chr16:69774200-69783800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr16:69774200-69785200	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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