Variant report

Variant	rs6688399
Chromosome Location	chr1:155722723-155722724
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155722602..155725038-chr1:155735095..155737903,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10796952	0.89[AMR][1000 genomes]
rs11264417	0.93[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs1621690	0.85[AFR][1000 genomes]
rs1625821	1.00[AMR][1000 genomes]
rs1627630	0.93[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs168343	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs171168	0.93[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1749412	0.93[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1749413	1.00[AMR][1000 genomes]
rs1749414	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1749420	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1749422	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1756242	0.93[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1765280	0.81[AFR][1000 genomes]
rs1765283	0.98[AFR][1000 genomes]
rs1765286	0.86[AFR][1000 genomes]
rs1886618	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2136920	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2175389	1.00[AMR][1000 genomes]
rs2363017	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs2481623	0.83[AFR][1000 genomes]
rs2485470	0.89[AFR][1000 genomes]
rs2485472	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2666828	0.89[AMR][1000 genomes]
rs2686264	0.89[AMR][1000 genomes]
rs2885676	0.93[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2988999	0.89[AMR][1000 genomes]
rs348184	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs348188	0.89[AMR][1000 genomes]
rs348189	0.89[AMR][1000 genomes]
rs348191	1.00[AMR][1000 genomes]
rs348193	0.89[AMR][1000 genomes]
rs348197	1.00[AMR][1000 genomes]
rs348199	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs348200	1.00[AMR][1000 genomes]
rs348207	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs348208	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs348209	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35264557	0.89[AMR][1000 genomes]
rs4581273	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs492669	0.89[AMR][1000 genomes]
rs4971058	0.89[AMR][1000 genomes]
rs512551	0.87[ASW][hapmap];0.80[LWK][hapmap];0.82[MKK][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs540380	0.93[ASW][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs568672	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs606755	1.00[AMR][1000 genomes]
rs607036	0.89[AMR][1000 genomes]
rs617232	0.89[AMR][1000 genomes]
rs6427290	0.85[AFR][1000 genomes]
rs670787	0.89[AMR][1000 genomes]
rs708607	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs708609	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs708613	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8179457	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs822013	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822014	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822017	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822021	0.93[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822023	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822024	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822027	0.93[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822479	0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822481	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822483	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822485	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822487	0.83[AFR][1000 genomes]
rs822492	1.00[AMR][1000 genomes]
rs822496	0.93[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs822498	0.93[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822521	0.87[ASW][hapmap];0.87[LWK][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap]
rs822522	1.00[AMR][1000 genomes]
rs866603	0.93[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9427219	0.89[AMR][1000 genomes]
rs9427222	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9427227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9427229	1.00[AFR][1000 genomes];1.00[AMR][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	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	esv3436971	chr1:155618172-155733386	Weak transcription Strong transcription Enhancers Active TSS Flanking 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	32 gene(s)	inside rSNPs	diseases
5	esv3338099	chr1:155618190-155733359	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv3065	chr1:155682768-155727524	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155715400-155723000	Weak transcription	Aorta	Aorta
2	chr1:155715400-155725600	Weak transcription	Fetal Brain Male	brain
3	chr1:155715400-155726200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:155715400-155730000	Weak transcription	Stomach Mucosa	stomach
5	chr1:155715400-155739200	Weak transcription	Fetal Heart	heart
6	chr1:155715400-155789200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:155715600-155722800	Weak transcription	Fetal Kidney	kidney
8	chr1:155715600-155722800	Weak transcription	Gastric	stomach
9	chr1:155715600-155725000	Weak transcription	Small Intestine	intestine
10	chr1:155715600-155725200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:155715600-155725200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:155715600-155725400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:155715600-155726800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:155715600-155764600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:155716000-155725000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:155716000-155793400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:155716200-155722800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:155716200-155722800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:155716200-155726800	Weak transcription	A549	lung
20	chr1:155716600-155725400	Strong transcription	Fetal Intestine Small	intestine
21	chr1:155716600-155781800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:155717200-155725000	Strong transcription	Lung	lung
23	chr1:155717200-155725600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:155717200-155761000	Strong transcription	Fetal Stomach	stomach
25	chr1:155717400-155731000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:155717400-155733400	Strong transcription	Brain Anterior Caudate	brain
27	chr1:155717400-155795800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:155717600-155733800	Strong transcription	Spleen	Spleen
29	chr1:155717600-155750200	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:155718000-155729400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:155718200-155729400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:155718400-155722800	Weak transcription	GM12878-XiMat	blood
33	chr1:155718600-155722800	Weak transcription	Pancreas	Pancrea
34	chr1:155718800-155722800	Weak transcription	HMEC	breast
35	chr1:155718800-155726800	Weak transcription	Psoas Muscle	Psoas
36	chr1:155719200-155722800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:155719200-155722800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:155719200-155723400	Weak transcription	NHDF-Ad	bronchial
39	chr1:155720000-155732000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr1:155720200-155732800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr1:155720200-155732800	Strong transcription	Osteobl	bone
42	chr1:155720200-155733000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr1:155720200-155733800	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:155720200-155745400	Strong transcription	Fetal Muscle Leg	muscle
45	chr1:155720200-155748600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:155720200-155748800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:155720200-155748800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr1:155720200-155749000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:155720200-155749600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:155720200-155750200	Strong transcription	Primary T cells from cord blood	blood

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