Variant report

Variant	rs7908539
Chromosome Location	chr10:43278659-43278660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:43046301..43049301-chr10:43278095..43279962,3	K562	blood:
2	chr10:43277481..43279174-chr8:144910550..144912585,2	MCF-7	breast:
3	chr10:43132020..43136600-chr10:43277441..43279853,5	MCF-7	breast:
4	chr10:43132257..43135644-chr10:43275563..43280155,11	MCF-7	breast:
5	chr10:43133575..43134141-chr10:43278109..43279018,2	MCF-7	breast:
6	chr10:43132863..43135217-chr10:43276470..43279459,4	K562	blood:
7	chr1:148241298..148242285-chr10:43278087..43278706,2	Hela-S3	cervix:
8	chr10:43278278..43279935-chr10:43297692..43300575,2	K562	blood:
9	chr10:43278401..43278901-chr12:52444991..52445906,2	Hela-S3	cervix:
10	chr10:43132954..43135205-chr10:43277445..43279937,2	K562	blood:
11	chr10:42969989..42972327-chr10:43278200..43280239,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000207501	Chromatin interaction
ENSG00000234420	Chromatin interaction
ENSG00000179950	Chromatin interaction
ENSG00000272373	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000196693	Chromatin interaction
ENSG00000185904	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1085783	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1091925	0.92[EUR][1000 genomes]
rs1342143	1.00[ASN][1000 genomes]
rs17158174	1.00[YRI][hapmap]
rs17158193	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159047	1.00[CEU][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159071	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17159198	1.00[CEU][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17344904	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17344997	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17345889	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17429275	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17429415	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17430796	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17431976	0.82[CEU][hapmap]
rs1775069	1.00[ASN][1000 genomes]
rs1935644	1.00[ASN][1000 genomes]
rs2078397	1.00[CEU][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744082	1.00[ASN][1000 genomes]
rs2795505	1.00[ASN][1000 genomes]
rs2796563	1.00[ASN][1000 genomes]
rs2796565	1.00[ASN][1000 genomes]
rs41295810	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515365	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61736599	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61842933	1.00[ASN][1000 genomes]
rs61842935	1.00[ASN][1000 genomes]
rs61843368	0.92[EUR][1000 genomes]
rs61843371	0.89[EUR][1000 genomes]
rs61843372	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61843373	1.00[ASN][1000 genomes]
rs61843374	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61843380	1.00[ASN][1000 genomes]
rs61843381	1.00[ASN][1000 genomes]
rs61843382	1.00[ASN][1000 genomes]
rs61843407	1.00[ASN][1000 genomes]
rs61843419	1.00[ASN][1000 genomes]
rs61843420	1.00[ASN][1000 genomes]
rs61843422	1.00[ASN][1000 genomes]
rs61843437	1.00[ASN][1000 genomes]
rs61843438	1.00[ASN][1000 genomes]
rs61843457	1.00[ASN][1000 genomes]
rs61843459	1.00[ASN][1000 genomes]
rs61843895	1.00[ASN][1000 genomes]
rs61843955	1.00[ASN][1000 genomes]
rs61843956	1.00[ASN][1000 genomes]
rs61843958	1.00[ASN][1000 genomes]
rs61843959	1.00[ASN][1000 genomes]
rs61844760	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61844763	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61844765	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844766	0.80[EUR][1000 genomes]
rs61844768	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844770	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61844771	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844772	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844774	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844775	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844813	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844814	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61844815	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844816	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844817	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844821	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844822	1.00[EUR][1000 genomes]
rs61844827	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844828	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844829	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844830	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61844832	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844835	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844837	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844848	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844849	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61844854	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61845260	1.00[ASN][1000 genomes]
rs61845261	1.00[ASN][1000 genomes]
rs61845262	1.00[ASN][1000 genomes]
rs61845264	1.00[ASN][1000 genomes]
rs61845265	1.00[ASN][1000 genomes]
rs61845963	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61845964	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638507	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593493	0.86[YRI][hapmap]
rs7089165	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7091439	1.00[CEU][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74135429	1.00[ASN][1000 genomes]
rs788248	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs788250	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs788286	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs788294	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7898007	0.92[YRI][hapmap]
rs7898266	0.92[YRI][hapmap]
rs7904220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7915796	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7923121	1.00[CEU][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv533331	chr10:42830221-43356410	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	esv2757381	chr10:43104068-43352995	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv34929	chr10:43116194-43329770	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv895076	chr10:43234432-43326627	Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1047838	chr10:43234590-43379219	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	nsv947889	chr10:43278237-43290003	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43277000-43279000	Active TSS	Stomach Mucosa	stomach
2	chr10:43277200-43278800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
3	chr10:43277200-43278800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
4	chr10:43277200-43278800	Active TSS	Primary T killer memory cells from peripheral blood	blood
5	chr10:43277200-43278800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr10:43277200-43278800	Active TSS	Brain Germinal Matrix	brain
7	chr10:43277200-43278800	Active TSS	Brain Substantia Nigra	brain
8	chr10:43277200-43278800	Active TSS	Colon Smooth Muscle	Colon
9	chr10:43277200-43278800	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr10:43277200-43278800	Active TSS	Fetal Kidney	kidney
11	chr10:43277200-43279000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr10:43277200-43279000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr10:43277200-43279000	Active TSS	Colonic Mucosa	Colon
14	chr10:43277200-43279000	Active TSS	Rectal Smooth Muscle	rectum
15	chr10:43277200-43279200	Active TSS	HSMM	muscle
16	chr10:43277200-43279400	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr10:43277200-43279400	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr10:43277200-43279400	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr10:43277200-43279400	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr10:43277200-43279400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr10:43277200-43279800	Active TSS	GM12878-XiMat	blood
22	chr10:43277400-43278800	Active TSS	Fetal Brain Female	brain
23	chr10:43277400-43279000	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr10:43277400-43279000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr10:43277400-43279000	Active TSS	HSMMtube	muscle
26	chr10:43277400-43279000	Active TSS	NHEK	skin
27	chr10:43277400-43279000	Active TSS	NHLF	lung
28	chr10:43277400-43279200	Active TSS	H9 Cell Line	embryonic stem cell
29	chr10:43277400-43279200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr10:43277400-43279200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr10:43277400-43279200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr10:43277400-43279200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr10:43277400-43279200	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr10:43277400-43279200	Active TSS	Ovary	ovary
35	chr10:43277400-43279400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr10:43277400-43279400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr10:43277400-43279400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr10:43277400-43279400	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr10:43277400-43279400	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr10:43277400-43279400	Active TSS	Fetal Intestine Large	intestine
41	chr10:43277400-43279400	Active TSS	Osteobl	bone
42	chr10:43277400-43279600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr10:43277400-43279800	Active TSS	A549	lung
44	chr10:43277600-43278800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr10:43277600-43278800	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr10:43277600-43278800	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr10:43277600-43278800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
48	chr10:43277600-43278800	Active TSS	Liver	Liver
49	chr10:43277600-43278800	Active TSS	Brain Cingulate Gyrus	brain
50	chr10:43277600-43278800	Active TSS	Brain Inferior Temporal Lobe	brain

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