Variant report

Variant	rs6587975
Chromosome Location	chr1:62851933-62851934
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	chr1:62851538..62854000-chr1:62900356..62902478,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162607	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10789110	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10889325	0.85[AMR][1000 genomes]
rs10889326	0.91[AMR][1000 genomes]
rs3861942	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4915833	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4915834	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6587974	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6687215	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6693540	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6699962	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7512888	0.85[AMR][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	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6587975	TM2D1	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62848000-62855400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:62848000-62871800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:62849400-62852000	Enhancers	Fetal Muscle Leg	muscle
4	chr1:62849600-62852000	Enhancers	Brain Substantia Nigra	brain
5	chr1:62849600-62852200	Enhancers	Fetal Stomach	stomach
6	chr1:62849800-62853000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:62849800-62853600	Enhancers	Hela-S3	cervix
8	chr1:62850000-62852400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:62850000-62852800	Enhancers	Adipose Nuclei	Adipose
10	chr1:62850000-62853400	Enhancers	Stomach Mucosa	stomach
11	chr1:62850200-62852800	Enhancers	Fetal Lung	lung
12	chr1:62850200-62853400	Enhancers	Fetal Intestine Large	intestine
13	chr1:62850200-62853400	Enhancers	Fetal Intestine Small	intestine
14	chr1:62850400-62852000	Enhancers	Fetal Heart	heart
15	chr1:62850400-62852800	Weak transcription	Pancreas	Pancrea
16	chr1:62850600-62852000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:62850600-62855400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:62851000-62852000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:62851000-62852000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:62851000-62852000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:62851000-62852000	Enhancers	Fetal Muscle Trunk	muscle
22	chr1:62851000-62852000	Weak transcription	HSMMtube	muscle
23	chr1:62851000-62852200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:62851400-62852600	Enhancers	Brain Germinal Matrix	brain
25	chr1:62851600-62852000	Enhancers	Fetal Thymus	thymus
26	chr1:62851600-62852600	Flanking Active TSS	HepG2	liver
27	chr1:62851600-62852800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr1:62851600-62852800	Enhancers	NH-A	brain
29	chr1:62851600-62853000	Enhancers	Liver	Liver
30	chr1:62851600-62853000	Enhancers	Fetal Kidney	kidney
31	chr1:62851800-62852000	Enhancers	Brain Angular Gyrus	brain
32	chr1:62851800-62852200	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr1:62851800-62852200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr1:62851800-62852200	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr1:62851800-62852400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr1:62851800-62852400	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr1:62851800-62852400	Enhancers	Brain Hippocampus Middle	brain
38	chr1:62851800-62852600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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