Variant report

Variant	rs17544868
Chromosome Location	chr6:38642889-38642890
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38641497..38643657-chr6:38669576..38672277,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124767	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10484855	0.88[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1130534	0.83[EUR][1000 genomes]
rs11751782	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206711	1.00[ASN][1000 genomes]
rs12212784	1.00[ASN][1000 genomes]
rs13191302	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194237	0.89[EUR][1000 genomes]
rs13196530	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196708	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198900	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13199033	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13202862	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13203443	0.88[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207160	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13209846	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210334	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13212218	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213257	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214969	0.90[EUR][1000 genomes]
rs13215896	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13217234	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13218305	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219252	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219395	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13219781	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1698998	1.00[ASN][1000 genomes]
rs17544311	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1937782	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2654449	1.00[ASN][1000 genomes]
rs28360530	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34349982	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34360712	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34408317	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34470929	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34519749	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34637217	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34695044	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34897279	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34962226	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34971977	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35147121	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35152718	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35207097	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35266471	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35364976	0.94[EUR][1000 genomes]
rs35388596	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35901431	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35975219	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67457665	1.00[ASN][1000 genomes]
rs6932648	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs71544423	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71571331	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71571332	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71571336	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72856580	1.00[ASN][1000 genomes]
rs73416349	1.00[ASN][1000 genomes]
rs73416350	1.00[ASN][1000 genomes]
rs73416351	1.00[ASN][1000 genomes]
rs7451595	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7604	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746400	1.00[ASN][1000 genomes]
rs7750789	1.00[ASN][1000 genomes]
rs7762397	1.00[ASN][1000 genomes]
rs9369075	0.81[EUR][1000 genomes]
rs9394523	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9394524	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9462450	0.81[EUR][1000 genomes]
rs963720	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	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
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2758049	chr6:38588969-38711085	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2759421	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv427754	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv428144	chr6:38588969-38711085	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38609000-38645200	Weak transcription	Fetal Intestine Small	intestine
2	chr6:38609000-38645600	Weak transcription	Left Ventricle	heart
3	chr6:38609200-38643400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:38609800-38643000	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:38612800-38648400	Weak transcription	Brain Anterior Caudate	brain
6	chr6:38612800-38652800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:38614800-38654800	Weak transcription	Brain Angular Gyrus	brain
8	chr6:38615200-38645200	Weak transcription	Ovary	ovary
9	chr6:38615200-38649400	Weak transcription	Fetal Brain Male	brain
10	chr6:38618200-38646200	Weak transcription	Aorta	Aorta
11	chr6:38618800-38643800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:38620200-38646200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:38621000-38643400	Weak transcription	Fetal Kidney	kidney
14	chr6:38622400-38643200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:38622400-38643800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:38623400-38645600	Weak transcription	Brain Substantia Nigra	brain
17	chr6:38624200-38646200	Weak transcription	Lung	lung
18	chr6:38624600-38643200	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:38626400-38645200	Weak transcription	Fetal Stomach	stomach
20	chr6:38629400-38644800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr6:38640000-38643000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:38640000-38649400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:38640000-38649400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr6:38640000-38652400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr6:38640200-38650200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:38641000-38646200	Weak transcription	Brain Germinal Matrix	brain
27	chr6:38641000-38646200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:38641000-38654800	Weak transcription	Fetal Heart	heart
29	chr6:38641200-38643000	Weak transcription	Placenta	Placenta
30	chr6:38641200-38644400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:38641200-38646200	Weak transcription	Esophagus	oesophagus
32	chr6:38641200-38670000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:38641400-38643000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr6:38641400-38643000	Weak transcription	A549	lung
35	chr6:38641400-38649400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:38641600-38646200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:38641600-38646200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr6:38641600-38646200	Weak transcription	Spleen	Spleen
39	chr6:38641600-38668000	Weak transcription	NHLF	lung
40	chr6:38641800-38643200	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr6:38641800-38643200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:38641800-38643600	Weak transcription	Primary B cells from cord blood	blood
43	chr6:38641800-38645600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr6:38641800-38645800	Weak transcription	Colonic Mucosa	Colon
45	chr6:38641800-38649400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr6:38641800-38650600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:38641800-38651000	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr6:38641800-38654800	Weak transcription	Pancreas	Pancrea
49	chr6:38642000-38643000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr6:38642000-38643000	Weak transcription	Monocytes-CD14+_RO01746	blood

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