Variant report

Variant	rs6682974
Chromosome Location	chr1:180847645-180847646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180846972..180853051-chr1:181055773..181063614,10	MCF-7	breast:
2	chr1:180847167..180849761-chr1:181110031..181112022,2	MCF-7	breast:
3	chr1:180842169..180845646-chr1:180846177..180849577,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162783	Chromatin interaction
ENSG00000272198	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10914096	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs11800333	0.90[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11812056	0.84[EUR][1000 genomes]
rs12085097	0.80[EUR][1000 genomes]
rs1339768	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs1970404	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs2331626	0.87[EUR][1000 genomes]
rs2331886	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs2944259	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2944262	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3002113	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3002114	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs3002115	0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3002116	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3002117	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs3002121	1.00[JPT][hapmap]
rs3002123	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3013633	0.89[EUR][1000 genomes]
rs3013634	0.89[EUR][1000 genomes]
rs3789366	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs3843278	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs3856058	0.87[EUR][1000 genomes]
rs4108558	0.91[EUR][1000 genomes]
rs66520411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6659049	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs67780680	0.92[EUR][1000 genomes]
rs72707408	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72723045	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7514404	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs7524547	0.88[EUR][1000 genomes]
rs7548318	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7550031	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9425881	1.00[CEU][hapmap];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180773400-180849200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:180773800-180853200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:180779800-180850800	Weak transcription	Small Intestine	intestine
4	chr1:180796400-180851000	Weak transcription	Fetal Intestine Small	intestine
5	chr1:180805800-180881000	Weak transcription	Aorta	Aorta
6	chr1:180812200-180867000	Weak transcription	Ovary	ovary
7	chr1:180819200-180851000	Weak transcription	Fetal Brain Male	brain
8	chr1:180822000-180862800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:180822800-180862800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:180823000-180854600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:180823600-180847800	Weak transcription	Primary T cells from cord blood	blood
12	chr1:180823600-180860000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:180823800-180851000	Weak transcription	Fetal Kidney	kidney
14	chr1:180823800-180851400	Weak transcription	Pancreas	Pancrea
15	chr1:180823800-180862600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:180824000-180848000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:180824000-180867600	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:180824000-180880800	Weak transcription	Right Ventricle	heart
19	chr1:180824200-180851000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:180827800-180856600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:180828000-180852400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:180828000-180853200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:180828000-180853200	Weak transcription	NHEK	skin
24	chr1:180828600-180867800	Weak transcription	HSMM	muscle
25	chr1:180828800-180851000	Weak transcription	Brain Germinal Matrix	brain
26	chr1:180830000-180867600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:180831000-180851400	Weak transcription	Fetal Thymus	thymus
28	chr1:180831200-180858600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:180831600-180847800	Weak transcription	Fetal Brain Female	brain
30	chr1:180831600-180851000	Weak transcription	Brain Angular Gyrus	brain
31	chr1:180831600-180852600	Weak transcription	Fetal Lung	lung
32	chr1:180832200-180848600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:180832400-180848000	Weak transcription	Fetal Heart	heart
34	chr1:180832400-180850000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:180832400-180850000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:180832400-180850800	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:180832400-180850800	Weak transcription	NH-A	brain
38	chr1:180832400-180851000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:180832400-180851000	Weak transcription	Brain Anterior Caudate	brain
40	chr1:180832400-180853200	Weak transcription	Fetal Stomach	stomach
41	chr1:180832600-180854400	Weak transcription	Liver	Liver
42	chr1:180832800-180861800	Weak transcription	HepG2	liver
43	chr1:180833200-180851000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:180834000-180849200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:180834200-180851000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:180834800-180855800	Weak transcription	Gastric	stomach
47	chr1:180835400-180862800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:180835600-180855400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:180835800-180856600	Weak transcription	Fetal Intestine Large	intestine
50	chr1:180835800-180858800	Weak transcription	Rectal Mucosa Donor 31	rectum

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