Variant report

Variant	rs12541231
Chromosome Location	chr8:38949532-38949533
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:38933732..38936418-chr8:38947721..38949546,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10089487	0.86[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs10113077	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs10958813	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11777149	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11777376	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11787126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11985898	0.81[MEX][hapmap]
rs12056655	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12543388	0.83[EUR][1000 genomes]
rs12543921	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12546318	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12548006	0.86[ASW][hapmap];0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12548416	0.83[EUR][1000 genomes]
rs12548948	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12549232	0.90[MEX][hapmap];0.82[TSI][hapmap]
rs12549547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13248324	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13256952	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13268394	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13274567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34070223	0.83[EUR][1000 genomes]
rs34138150	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34185462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35391544	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35534138	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4129095	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4236757	0.82[TSI][hapmap]
rs4495395	0.81[CHB][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs4543512	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4733897	0.81[JPT][hapmap]
rs4733901	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4733905	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4733964	0.81[JPT][hapmap]
rs4733970	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6474516	0.81[JPT][hapmap]
rs66925354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7832578	0.81[CHB][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs7838874	0.81[CHB][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap]
rs9643858	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9643902	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9643904	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9643906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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	nsv1021581	chr8:38934014-39043954	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12541231	TM2D2	cis	parietal	SCAN
rs12541231	ADAM32	cis	cerebellum	SCAN
rs12541231	PLEKHA2	cis	lymphoblastoid	seeQTL
rs12541231	DDHD2	cis	cerebellum	SCAN
rs12541231	TM2D2	cis	cerebellum	SCAN
rs12541231	SGK196	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:38897400-38963400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:38905000-38960000	Weak transcription	HSMMtube	muscle
3	chr8:38911800-38964800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:38914400-38964800	Weak transcription	Fetal Kidney	kidney
5	chr8:38914800-38964800	Weak transcription	Colonic Mucosa	Colon
6	chr8:38918000-38962600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr8:38919000-38952600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr8:38919000-38970400	Weak transcription	K562	blood
9	chr8:38919600-38964800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr8:38920600-38963200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr8:38920800-38964800	Weak transcription	Fetal Brain Male	brain
12	chr8:38921000-38964800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr8:38921000-38965000	Weak transcription	Gastric	stomach
14	chr8:38921600-38964800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr8:38922000-38950400	Weak transcription	Fetal Brain Female	brain
16	chr8:38926200-38963600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr8:38929800-38950600	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr8:38932400-38964800	Weak transcription	Brain Germinal Matrix	brain
19	chr8:38933600-38951400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr8:38934000-38960800	Weak transcription	Colon Smooth Muscle	Colon
21	chr8:38935600-38960200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr8:38935600-38964800	Weak transcription	Brain Anterior Caudate	brain
23	chr8:38935800-38958800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr8:38939200-38964800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr8:38940400-38950600	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr8:38941400-38960000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr8:38941600-38956200	Weak transcription	GM12878-XiMat	blood
28	chr8:38941600-38960600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr8:38941600-38964800	Weak transcription	Psoas Muscle	Psoas
30	chr8:38943200-38950000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr8:38944000-38950200	Strong transcription	Osteobl	bone
32	chr8:38944000-38950800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr8:38944200-38950000	Strong transcription	Fetal Intestine Large	intestine
34	chr8:38944600-38965000	Weak transcription	Esophagus	oesophagus
35	chr8:38945200-38964800	Weak transcription	Fetal Heart	heart
36	chr8:38946400-38950600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr8:38946400-38950600	Strong transcription	HepG2	liver
38	chr8:38946400-38954400	Strong transcription	HUVEC	blood vessel
39	chr8:38946600-38949600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr8:38946600-38964800	Weak transcription	Small Intestine	intestine
41	chr8:38946800-38950200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr8:38946800-38950600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr8:38946800-38950600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr8:38946800-38950800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr8:38946800-38951200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr8:38946800-38951400	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr8:38946800-38964800	Weak transcription	Fetal Intestine Small	intestine
48	chr8:38946800-38964800	Weak transcription	Stomach Mucosa	stomach
49	chr8:38947000-38949600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr8:38947000-38949600	Strong transcription	Duodenum Smooth Muscle	Duodenum

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