Variant report

Variant	rs6692054
Chromosome Location	chr1:225651400-225651401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225649550..225651644-chr1:225657315..225659303,2	MCF-7	breast:
2	chr1:225646305..225648757-chr1:225649524..225652760,3	K562	blood:
3	chr1:225615091..225616977-chr1:225649695..225651542,2	MCF-7	breast:
4	chr1:225597465..225599804-chr1:225650818..225652643,4	K562	blood:
5	chr1:225597626..225599804-chr1:225650818..225652643,2	K562	blood:

Variant related genes	Relation type
ENSG00000143815	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10799310	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799312	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10799320	0.80[ASN][1000 genomes]
rs10915831	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10915836	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12034829	0.84[ASN][1000 genomes]
rs1222434	0.85[EUR][1000 genomes]
rs1222439	0.85[EUR][1000 genomes]
rs12742313	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1336480	0.81[EUR][1000 genomes]
rs1340865	0.93[ASN][1000 genomes]
rs1360958	0.81[EUR][1000 genomes]
rs1764345	0.83[EUR][1000 genomes]
rs1764347	0.83[EUR][1000 genomes]
rs1771318	0.83[EUR][1000 genomes]
rs1891000	0.84[ASN][1000 genomes]
rs2039620	0.87[ASN][1000 genomes]
rs2185528	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766930	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3856157	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3893032	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4233220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4554690	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653638	0.87[EUR][1000 genomes]
rs4653640	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs499385	0.81[EUR][1000 genomes]
rs6426075	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6702641	0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7522622	0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7527014	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7527184	0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7529690	0.82[ASN][1000 genomes]
rs7536925	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7545317	0.82[EUR][1000 genomes]
rs7548473	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7550784	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7552953	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs954534	0.83[EUR][1000 genomes]
rs9725758	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer 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	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225642400-225653000	Weak transcription	Primary B cells from cord blood	blood
2	chr1:225642400-225655200	Weak transcription	Small Intestine	intestine
3	chr1:225642600-225655000	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:225642800-225652800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:225646400-225653600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:225647000-225651600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr1:225647000-225651600	Enhancers	Fetal Muscle Leg	muscle
8	chr1:225647000-225653600	Enhancers	Esophagus	oesophagus
9	chr1:225647000-225654600	Enhancers	Fetal Thymus	thymus
10	chr1:225647000-225654800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:225647200-225651600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr1:225647400-225654800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr1:225647600-225652000	Enhancers	Fetal Stomach	stomach
14	chr1:225647600-225653800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:225647800-225653400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:225648000-225651400	Enhancers	Fetal Brain Male	brain
17	chr1:225648000-225652600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:225648400-225653400	Weak transcription	Fetal Intestine Large	intestine
19	chr1:225648600-225652800	Weak transcription	Fetal Kidney	kidney
20	chr1:225648800-225651400	Enhancers	Ovary	ovary
21	chr1:225648800-225652000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
22	chr1:225648800-225652200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:225648800-225652600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:225648800-225652600	Weak transcription	Osteobl	bone
25	chr1:225648800-225654600	Weak transcription	HUVEC	blood vessel
26	chr1:225649000-225652600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:225649000-225653200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:225649000-225654600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:225649200-225652000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr1:225649200-225652400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:225649200-225652800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:225649200-225654400	Weak transcription	Primary T cells from cord blood	blood
33	chr1:225649400-225653400	Weak transcription	Dnd41	blood
34	chr1:225649600-225652600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:225649800-225654800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:225649800-225662600	Weak transcription	Pancreas	Pancrea
37	chr1:225650000-225651400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:225650000-225651800	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr1:225650000-225652600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:225650000-225653200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:225650000-225653600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:225650200-225651600	Flanking Active TSS	Brain Germinal Matrix	brain
43	chr1:225650200-225651600	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr1:225650200-225652000	Enhancers	Rectal Smooth Muscle	rectum
45	chr1:225650200-225653200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:225650200-225653200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr1:225650200-225653800	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr1:225650200-225654600	Weak transcription	Spleen	Spleen
49	chr1:225650400-225651400	Enhancers	Adipose Nuclei	Adipose
50	chr1:225650400-225651400	Enhancers	Lung	lung

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