Variant report

Variant	rs16890299
Chromosome Location	chr6:37960055-37960056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37948324..37950868-chr6:37959290..37962178,2	MCF-7	breast:
2	chr6:37959253..37960891-chr6:37963216..37966169,3	K562	blood:
3	chr6:37956692..37960891-chr6:37962737..37966006,6	K562	blood:

Extended variants
information (count: 141 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10485030	0.85[CHB][hapmap]
rs10498739	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10498740	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10947702	0.85[CHB][hapmap]
rs10947704	0.85[CHB][hapmap]
rs10947710	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11750950	0.95[CHB][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs11751781	0.85[CHB][hapmap]
rs11752521	0.85[CHB][hapmap]
rs11752863	0.94[ASN][1000 genomes]
rs11753054	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11755629	0.85[CHB][hapmap]
rs11756713	0.85[CHB][hapmap]
rs11756902	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11757072	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11757323	0.94[ASN][1000 genomes]
rs11758095	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11759483	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11759725	0.93[ASN][1000 genomes]
rs11759826	0.85[CHB][hapmap]
rs12660221	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12660498	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12660732	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12660773	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12660922	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12661073	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12661109	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12661129	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12661378	0.85[CHB][hapmap]
rs12661480	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12662305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs12662426	0.85[CHB][hapmap]
rs12662823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12663086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12663207	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12663427	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12663957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12664091	0.85[CHB][hapmap]
rs12664768	0.85[CHB][hapmap]
rs12664900	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13206035	0.85[CHB][hapmap]
rs16890175	0.90[CHB][hapmap]
rs16890177	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs16890181	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs16890215	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs16890247	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16890298	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16890301	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs16890305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16890307	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16890309	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16890341	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs16890362	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16890370	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1885324	0.90[CHB][hapmap]
rs2055207	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2055208	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2064795	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2145887	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2273441	0.85[CHB][hapmap]
rs2274090	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2274091	0.85[CHB][hapmap]
rs2395689	0.90[CHB][hapmap]
rs2395692	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2395693	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2645111	0.81[ASN][1000 genomes]
rs2645125	0.84[ASN][1000 genomes]
rs2842510	0.85[CHB][hapmap]
rs2842511	0.90[CHB][hapmap]
rs2842521	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs28740822	0.94[ASN][1000 genomes]
rs34370874	0.94[ASN][1000 genomes]
rs35051126	0.81[ASN][1000 genomes]
rs3800364	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3844314	0.85[CHB][hapmap]
rs3852216	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4524602	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs55786703	0.98[ASN][1000 genomes]
rs56348433	0.94[ASN][1000 genomes]
rs56390138	0.94[ASN][1000 genomes]
rs57160603	0.94[ASN][1000 genomes]
rs57198506	1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs57276677	0.93[ASN][1000 genomes]
rs57458792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57591988	0.96[ASN][1000 genomes]
rs57911756	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs57995712	0.94[ASN][1000 genomes]
rs58084785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs58320470	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58473303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58692659	1.00[AMR][1000 genomes]
rs59036086	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59103990	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs59649654	1.00[AMR][1000 genomes]
rs59769374	0.94[ASN][1000 genomes]
rs59859268	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59996041	0.99[ASN][1000 genomes]
rs60141491	0.80[ASN][1000 genomes]
rs60284537	1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs60404082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60508820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60637081	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs60883115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61090283	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61108907	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61277916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61332486	1.00[AMR][1000 genomes]
rs61466900	1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6458032	0.85[CHB][hapmap]
rs6911716	0.85[CHB][hapmap]
rs71569402	0.82[ASN][1000 genomes]
rs73421436	0.94[ASN][1000 genomes]
rs73421439	0.94[ASN][1000 genomes]
rs752110	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7739801	0.94[CHB][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs7742226	0.84[CHB][hapmap]
rs7746266	0.84[CHB][hapmap]
rs7748312	0.85[CHB][hapmap]
rs7748392	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7756261	0.85[CHB][hapmap]
rs7759792	0.85[CHB][hapmap]
rs7761561	0.81[CHB][hapmap]
rs7764130	0.85[CHB][hapmap]
rs7773419	0.85[CHB][hapmap]
rs7775794	0.85[CHB][hapmap]
rs874095	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs876818	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9470772	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9470777	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9470784	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9470794	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9470798	0.94[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv602956	chr6:37909084-37986489	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2761037	chr6:37930659-37966762	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37949800-37962000	Weak transcription	Small Intestine	intestine
2	chr6:37950000-37963600	Weak transcription	Spleen	Spleen
3	chr6:37952200-37961400	Enhancers	Liver	Liver
4	chr6:37953400-37960400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:37953400-37962600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:37953400-37962600	Weak transcription	Lung	lung
7	chr6:37953400-37965200	Weak transcription	Esophagus	oesophagus
8	chr6:37954000-37960200	Enhancers	Colon Smooth Muscle	Colon
9	chr6:37954000-37960600	Enhancers	HSMM	muscle
10	chr6:37954200-37963000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:37954400-37960200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr6:37954600-37960200	Enhancers	NHLF	lung
13	chr6:37955400-37960400	Enhancers	Adipose Nuclei	Adipose
14	chr6:37955400-37960400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr6:37955400-37960400	Enhancers	Stomach Smooth Muscle	stomach
16	chr6:37955400-37960800	Enhancers	Rectal Smooth Muscle	rectum
17	chr6:37955600-37963800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:37956200-37961800	Weak transcription	Fetal Brain Female	brain
19	chr6:37956200-37962000	Weak transcription	Fetal Stomach	stomach
20	chr6:37956200-37965400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr6:37956200-37978800	Weak transcription	Primary T cells from cord blood	blood
22	chr6:37956400-37960200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:37956400-37961400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:37956600-37961800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:37956600-37961800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr6:37956600-37962000	Weak transcription	Brain Angular Gyrus	brain
27	chr6:37956600-37962000	Weak transcription	Fetal Kidney	kidney
28	chr6:37956600-37967200	Weak transcription	Primary B cells from cord blood	blood
29	chr6:37956800-37960200	Enhancers	GM12878-XiMat	blood
30	chr6:37956800-37961600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr6:37956800-37962000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr6:37957600-37960400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr6:37957600-37961800	Weak transcription	Brain Germinal Matrix	brain
34	chr6:37957600-37962200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:37957600-37962400	Weak transcription	Pancreas	Pancrea
36	chr6:37957800-37960200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:37957800-37960600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:37957800-37961600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:37957800-37962200	Weak transcription	Fetal Brain Male	brain
40	chr6:37957800-37976400	Weak transcription	Aorta	Aorta
41	chr6:37958000-37960400	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr6:37958000-37961600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr6:37958000-37961800	Weak transcription	Fetal Lung	lung
44	chr6:37958600-37960600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:37958800-37960200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr6:37958800-37961600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr6:37958800-37961800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:37958800-37961800	Weak transcription	Brain Anterior Caudate	brain
49	chr6:37958800-37963200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr6:37959000-37960600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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