Variant report

Variant	rs6728401
Chromosome Location	chr2:180028785-180028786
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	chr2:180027947..180030148-chr2:180031681..180034023,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10497535	0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11897308	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11901421	0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11903685	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11904657	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1490997	0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16866635	0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16866636	0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16866667	0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2044477	0.83[AFR][1000 genomes]
rs3731739	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs3816345	0.92[YRI][hapmap]
rs6433758	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6433762	0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6433763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6433765	0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6707001	0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6710100	0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6723850	0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7566810	0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs930620	0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv3060	chr2:179990791-180035511	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv1807721	chr2:180024167-180076733	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
4	chr2:179980000-180038800	Weak transcription	HMEC	breast
5	chr2:179980000-180056800	Weak transcription	HSMM	muscle
6	chr2:179986600-180030400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:179991600-180043200	Weak transcription	Psoas Muscle	Psoas
8	chr2:179996200-180047600	Weak transcription	NH-A	brain
9	chr2:179998000-180060600	Weak transcription	Right Ventricle	heart
10	chr2:180002400-180030200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:180003200-180039800	Weak transcription	Brain Germinal Matrix	brain
12	chr2:180004800-180046000	Weak transcription	Spleen	Spleen
13	chr2:180005000-180028800	Weak transcription	Hela-S3	cervix
14	chr2:180005600-180040200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:180005600-180044400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:180005600-180044400	Weak transcription	Esophagus	oesophagus
17	chr2:180005800-180030200	Weak transcription	Thymus	Thymus
18	chr2:180005800-180043200	Weak transcription	Fetal Brain Male	brain
19	chr2:180005800-180053600	Weak transcription	Primary T cells from cord blood	blood
20	chr2:180006000-180030600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:180006000-180044600	Weak transcription	Pancreas	Pancrea
22	chr2:180006200-180031400	Weak transcription	Brain Hippocampus Middle	brain
23	chr2:180006200-180031400	Weak transcription	Fetal Brain Female	brain
24	chr2:180006400-180030200	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:180006600-180042000	Weak transcription	Brain Substantia Nigra	brain
26	chr2:180006600-180051000	Weak transcription	HUVEC	blood vessel
27	chr2:180006800-180031600	Weak transcription	Brain Anterior Caudate	brain
28	chr2:180006800-180054600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:180007400-180035200	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:180007400-180035600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:180007400-180042200	Weak transcription	Brain Angular Gyrus	brain
32	chr2:180007400-180043000	Weak transcription	Aorta	Aorta
33	chr2:180007600-180030400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:180007600-180031000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:180007600-180031200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:180008400-180030600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:180008400-180042200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:180008600-180029400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr2:180008600-180037600	Weak transcription	Fetal Thymus	thymus
40	chr2:180008600-180038400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:180008600-180048400	Weak transcription	Small Intestine	intestine
42	chr2:180011200-180029000	Weak transcription	Dnd41	blood
43	chr2:180011800-180039400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:180013200-180044400	Weak transcription	Fetal Kidney	kidney
45	chr2:180015000-180041600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:180015000-180043200	Weak transcription	Gastric	stomach
47	chr2:180015000-180054800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:180015000-180056000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:180015000-180060600	Weak transcription	Lung	lung
50	chr2:180015200-180039600	Weak transcription	Fetal Lung	lung

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