Variant report

Variant	rs549852
Chromosome Location	chr6:74324403-74324404
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:74221323..74236726-chr6:74306065..74338770,101	K562	blood:
2	chr6:74236818..74238643-chr6:74323624..74325300,2	K562	blood:
3	chr6:74221668..74234853-chr6:74311080..74327130,62	K562	blood:
4	chr6:74219940..74235097-chr6:74314890..74324923,44	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156508	Chromatin interaction
ENSG00000223967	Chromatin interaction
ENSG00000229862	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs12192512	0.82[EUR][1000 genomes]
rs12212323	0.81[EUR][1000 genomes]
rs1245333	0.80[EUR][1000 genomes]
rs1303141	0.80[EUR][1000 genomes]
rs1691343	0.85[EUR][1000 genomes]
rs1691344	0.83[EUR][1000 genomes]
rs1691345	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1691347	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1691348	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1691350	0.81[AFR][1000 genomes]
rs1703459	0.82[ASN][1000 genomes]
rs1703460	0.84[ASN][1000 genomes]
rs1703463	0.86[EUR][1000 genomes]
rs1703467	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs1741889	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs1741891	0.86[EUR][1000 genomes]
rs1741898	0.85[EUR][1000 genomes]
rs2500219	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs2753185	0.82[EUR][1000 genomes]
rs382038	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs382041	0.82[EUR][1000 genomes]
rs3846751	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs395996	0.82[EUR][1000 genomes]
rs4032316	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4032317	0.92[YRI][hapmap]
rs435132	0.82[EUR][1000 genomes]
rs445098	0.89[EUR][1000 genomes]
rs473473	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs475459	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs475461	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476996	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs478301	0.83[AFR][1000 genomes]
rs478836	0.82[EUR][1000 genomes]
rs480714	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs480871	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs485802	0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs487673	0.94[AFR][1000 genomes]
rs495385	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs498907	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs498990	0.92[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs535502	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs546134	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs549892	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs560386	0.83[AFR][1000 genomes]
rs560797	0.85[EUR][1000 genomes]
rs562131	0.95[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs565535	0.81[EUR][1000 genomes]
rs573753	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs583443	0.92[CEU][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs605567	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs612800	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs615052	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs615956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438457	0.80[ASN][1000 genomes]
rs628038	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs629381	0.96[YRI][hapmap]
rs642651	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs664953	0.86[ASN][1000 genomes]
rs676464	0.88[EUR][1000 genomes]
rs676952	0.80[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7449500	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs780066	0.81[EUR][1000 genomes]
rs9442934	0.89[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs9446972	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1017716	chr6:74173173-74401162	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
6	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	nsv527357	chr6:74253266-74325403	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv603694	chr6:74275405-74365807	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv1029927	chr6:74300496-74424355	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
11	nsv1027691	chr6:74302980-74417450	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
12	nsv886160	chr6:74305276-74341589	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74290600-74338800	Weak transcription	Ovary	ovary
2	chr6:74296200-74332000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:74296400-74325800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:74296400-74354800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:74296400-74354800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:74296400-74355000	Weak transcription	Fetal Brain Male	brain
7	chr6:74296600-74344000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:74296800-74334000	Weak transcription	Fetal Lung	lung
9	chr6:74297000-74361800	Weak transcription	GM12878-XiMat	blood
10	chr6:74303400-74355000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:74307200-74362400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:74307600-74356400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:74308000-74340200	Weak transcription	Brain Substantia Nigra	brain
14	chr6:74308400-74329000	Weak transcription	NHEK	skin
15	chr6:74311200-74355000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr6:74311800-74324800	Weak transcription	K562	blood
17	chr6:74312600-74332400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr6:74313200-74325000	Strong transcription	Fetal Intestine Large	intestine
19	chr6:74313200-74331800	Strong transcription	Fetal Muscle Leg	muscle
20	chr6:74313800-74331200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr6:74314200-74362800	Weak transcription	Stomach Mucosa	stomach
22	chr6:74314400-74346400	Weak transcription	Psoas Muscle	Psoas
23	chr6:74315000-74326000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:74315200-74348800	Weak transcription	HMEC	breast
25	chr6:74315400-74345200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr6:74315600-74362800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:74316000-74325400	Strong transcription	Primary T cells from cord blood	blood
28	chr6:74316200-74347000	Strong transcription	Fetal Intestine Small	intestine
29	chr6:74316400-74349200	Weak transcription	HUVEC	blood vessel
30	chr6:74316600-74355000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:74318400-74350000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:74318400-74355000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:74318800-74324600	Weak transcription	Small Intestine	intestine
34	chr6:74318800-74355200	Weak transcription	Colonic Mucosa	Colon
35	chr6:74319000-74341200	Weak transcription	NH-A	brain
36	chr6:74319600-74354800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:74319800-74340000	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:74319800-74354800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:74320400-74340200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:74320600-74324600	Weak transcription	A549	lung
41	chr6:74320600-74328600	Weak transcription	Hela-S3	cervix
42	chr6:74320800-74331200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:74320800-74341200	Weak transcription	Brain Angular Gyrus	brain
44	chr6:74321200-74325000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:74321200-74325000	Strong transcription	Left Ventricle	heart
46	chr6:74321200-74329400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:74321200-74332000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr6:74321400-74325000	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:74321400-74331800	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr6:74321600-74325000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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