Variant report

Variant	rs4129095
Chromosome Location	chr8:38896721-38896722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:38853640..38855398-chr8:38893873..38896745,2	MCF-7	breast:
2	chr8:38895697..38898348-chr8:38953067..38955793,2	K562	blood:

Variant related genes	Relation type
ENSG00000168615	Chromatin interaction
ENSG00000169490	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10086693	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10089487	0.86[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs10113077	0.81[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs10958813	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11777149	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11777376	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11787126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[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];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12541231	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]
rs12543921	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12546318	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][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];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12548948	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12549232	0.94[MEX][hapmap];0.82[TSI][hapmap]
rs12549547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13248324	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][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];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[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];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13274567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13282047	0.81[EUR][1000 genomes]
rs34138150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34185462	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35391544	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35534138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4543512	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4733897	0.81[JPT][hapmap]
rs4733901	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][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];1.00[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]
rs4733964	0.81[JPT][hapmap]
rs4733970	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6474516	0.81[JPT][hapmap]
rs66925354	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7832578	0.81[CHB][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs7838874	0.81[CHB][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs9643858	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9643902	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9643906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[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	esv3445313	chr8:38886844-38936643	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4129095	DDHD2	cis	cerebellum	SCAN
rs4129095	TM2D2	cis	cerebellum	SCAN
rs4129095	ADAM32	cis	cerebellum	SCAN
rs4129095	TM2D2	cis	parietal	SCAN
rs4129095	PLEKHA2	cis	lymphoblastoid	seeQTL
rs4129095	SGK196	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:38869600-38902800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:38882000-38913600	Weak transcription	Fetal Kidney	kidney
3	chr8:38883000-38913000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr8:38885000-38899400	Weak transcription	Liver	Liver
5	chr8:38885200-38902800	Weak transcription	Psoas Muscle	Psoas
6	chr8:38885400-38904400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr8:38885600-38903600	Weak transcription	Fetal Brain Female	brain
8	chr8:38885800-38911200	Weak transcription	Ovary	ovary
9	chr8:38886000-38899400	Weak transcription	Brain Substantia Nigra	brain
10	chr8:38886400-38904400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr8:38887400-38911200	Weak transcription	Aorta	Aorta
12	chr8:38888000-38899600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr8:38888200-38897000	Weak transcription	Fetal Intestine Large	intestine
14	chr8:38888200-38904400	Weak transcription	GM12878-XiMat	blood
15	chr8:38888400-38905400	Weak transcription	Primary B cells from cord blood	blood
16	chr8:38888800-38901600	Weak transcription	Fetal Brain Male	brain
17	chr8:38889000-38899600	Weak transcription	Fetal Lung	lung
18	chr8:38890000-38904400	Weak transcription	Gastric	stomach
19	chr8:38890200-38904400	Weak transcription	Esophagus	oesophagus
20	chr8:38890200-38911200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr8:38890200-38914400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr8:38890400-38897000	Enhancers	NHLF	lung
23	chr8:38890400-38903400	Weak transcription	Fetal Muscle Leg	muscle
24	chr8:38890400-38904200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr8:38890400-38904200	Weak transcription	Fetal Intestine Small	intestine
26	chr8:38890400-38904200	Weak transcription	Lung	lung
27	chr8:38890400-38919800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr8:38892600-38901000	Weak transcription	Dnd41	blood
29	chr8:38895000-38896800	Enhancers	Adipose Nuclei	Adipose
30	chr8:38895000-38896800	Enhancers	Small Intestine	intestine
31	chr8:38895000-38897000	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr8:38895000-38897400	Enhancers	Rectal Smooth Muscle	rectum
33	chr8:38895000-38897600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr8:38895000-38897600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr8:38895000-38897600	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr8:38895000-38897600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr8:38895200-38896800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr8:38895200-38896800	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr8:38895200-38896800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr8:38895200-38897200	Enhancers	Brain Anterior Caudate	brain
41	chr8:38895200-38897200	Flanking Active TSS	HUVEC	blood vessel
42	chr8:38895200-38897400	Enhancers	Colon Smooth Muscle	Colon
43	chr8:38895200-38897400	Enhancers	Stomach Mucosa	stomach
44	chr8:38895200-38897600	Enhancers	Stomach Smooth Muscle	stomach
45	chr8:38895200-38898400	Enhancers	Placenta Amnion	Placenta Amnion
46	chr8:38895400-38896800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr8:38895400-38896800	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr8:38895400-38897200	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr8:38895400-38897200	Flanking Active TSS	NH-A	brain
50	chr8:38895400-38897400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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