Variant report

Variant	rs688176
Chromosome Location	chr6:4068109-4068110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4063965..4066148-chr6:4066336..4068654,2	MCF-7	breast:
2	chr6:4067254..4070253-chr6:4071525..4075483,4	K562	blood:
3	chr6:4063481..4065487-chr6:4065794..4068948,3	K562	blood:
4	chr6:4064462..4068135-chr6:4134400..4138606,5	K562	blood:
5	chr6:4066739..4069378-chr6:4083684..4085264,2	MCF-7	breast:
6	chr6:4067620..4070166-chr6:4130566..4132778,2	K562	blood:
7	chr6:4063868..4065487-chr6:4067448..4070082,2	K562	blood:

Variant related genes	Relation type
ENSG00000254821	Chromatin interaction
ENSG00000234817	Chromatin interaction
ENSG00000198721	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs101418	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11755877	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs1204951	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2326408	0.83[ASN][1000 genomes]
rs2473597	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2745453	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2745455	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2783063	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[MEX][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2783073	0.83[ASN][1000 genomes]
rs582008	0.80[CHB][hapmap]
rs583782	0.80[CHB][hapmap]
rs583881	0.80[CHB][hapmap]
rs584585	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs588158	0.86[ASN][1000 genomes]
rs589494	0.83[ASN][1000 genomes]
rs590675	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs592953	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs593291	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs594662	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs595413	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs608195	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[ASN][1000 genomes]
rs609946	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs611500	0.83[ASN][1000 genomes]
rs612022	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs612477	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs613028	0.84[ASN][1000 genomes]
rs613260	0.83[ASN][1000 genomes]
rs613709	0.83[ASN][1000 genomes]
rs617604	0.91[ASN][1000 genomes]
rs617790	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs619439	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs619483	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs619873	0.83[ASN][1000 genomes]
rs620484	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs620901	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs623861	0.81[MEX][hapmap];0.80[YRI][hapmap]
rs626080	0.84[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs627259	0.89[ASN][1000 genomes]
rs629362	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs633290	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs634114	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.92[ASN][1000 genomes]
rs634698	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs634970	0.80[CHB][hapmap]
rs638329	0.80[CHB][hapmap]
rs639905	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs643232	0.90[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs646385	0.80[CHB][hapmap]
rs648900	0.83[ASN][1000 genomes]
rs649725	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs650183	0.93[CEU][hapmap];0.81[CHB][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs651246	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs653431	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs654621	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs654982	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs659025	1.00[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs659305	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs6597028	0.93[CEU][hapmap]
rs660560	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs661404	0.95[CHB][hapmap];0.83[CHD][hapmap];0.83[ASN][1000 genomes]
rs661657	0.91[ASN][1000 genomes]
rs662834	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs664299	0.81[ASN][1000 genomes]
rs664839	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs665728	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[MEX][hapmap];0.92[ASN][1000 genomes]
rs665894	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs666254	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs668070	0.86[ASN][1000 genomes]
rs670932	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs671364	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs674543	0.88[ASN][1000 genomes]
rs676683	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs678285	0.80[CHB][hapmap]
rs679303	0.80[CHB][hapmap]
rs682063	0.80[ASW][hapmap];0.93[CEU][hapmap];0.81[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs689308	0.83[ASN][1000 genomes]
rs694903	0.89[ASN][1000 genomes]
rs707991	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[ASN][1000 genomes]
rs7166	0.83[ASN][1000 genomes]
rs7744628	0.95[CHB][hapmap];0.80[CHD][hapmap];0.83[ASN][1000 genomes]
rs7756630	0.87[ASN][1000 genomes]
rs7757606	0.83[ASN][1000 genomes]
rs853416	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs853417	0.83[ASN][1000 genomes]
rs9328220	0.83[ASN][1000 genomes]
rs9378395	0.97[ASN][1000 genomes]
rs9405219	0.91[ASN][1000 genomes]
rs942475	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv462615	chr6:4052383-4096678	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv600860	chr6:4052383-4096678	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4023400-4071600	Weak transcription	Stomach Mucosa	stomach
2	chr6:4058200-4075000	Weak transcription	Small Intestine	intestine
3	chr6:4060400-4068200	Weak transcription	Ovary	ovary
4	chr6:4061600-4068600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:4063000-4073000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:4063400-4068200	Weak transcription	Fetal Lung	lung
7	chr6:4063400-4078800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:4063600-4072000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:4063800-4068200	Weak transcription	Fetal Brain Male	brain
10	chr6:4063800-4068600	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:4063800-4073200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:4064000-4068800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:4064000-4077600	Weak transcription	Brain Anterior Caudate	brain
14	chr6:4064200-4068200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:4065200-4069400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:4065200-4077400	Weak transcription	Brain Substantia Nigra	brain
17	chr6:4065600-4068400	Weak transcription	Fetal Kidney	kidney
18	chr6:4065600-4069000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:4065800-4068200	Weak transcription	Placenta	Placenta
20	chr6:4065800-4068600	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:4065800-4069000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr6:4065800-4069200	Weak transcription	K562	blood
23	chr6:4065800-4069600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:4066000-4068200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr6:4066000-4068200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr6:4066000-4068200	Weak transcription	HSMMtube	muscle
27	chr6:4066000-4068600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:4066000-4071000	Weak transcription	Gastric	stomach
29	chr6:4066000-4071200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:4066000-4077400	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:4066200-4068200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:4066200-4068200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:4066200-4068200	Weak transcription	Fetal Intestine Large	intestine
34	chr6:4066200-4068200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr6:4066200-4069200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr6:4066200-4069200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr6:4066200-4073000	Weak transcription	HUVEC	blood vessel
38	chr6:4066200-4077400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:4066400-4068200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:4066400-4068200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr6:4066400-4068200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:4066400-4068200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr6:4066400-4068600	Enhancers	HepG2	liver
44	chr6:4066400-4068800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr6:4066400-4069000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr6:4066400-4069800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:4066400-4077200	Weak transcription	Adipose Nuclei	Adipose
48	chr6:4066400-4077400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:4066600-4068200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:4066600-4068400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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