Variant report

Variant	rs6902994
Chromosome Location	chr6:36615675-36615676
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	chr6:36597486..36599707-chr6:36615187..36618681,3	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1321312	0.91[CEU][hapmap];0.89[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1969701	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1977172	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3176330	0.83[ASN][1000 genomes]
rs3176331	0.83[CHD][hapmap];0.93[GIH][hapmap]
rs3829966	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3829967	0.84[ASN][1000 genomes]
rs3829968	0.82[ASN][1000 genomes]
rs4135234	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4135237	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4135239	0.84[ASN][1000 genomes]
rs4713997	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4714000	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs6457936	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6907801	0.91[CEU][hapmap];0.89[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926780	0.90[CEU][hapmap];0.89[CHB][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7452626	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs762623	0.91[CHD][hapmap];0.93[GIH][hapmap];0.84[ASN][1000 genomes]
rs9380585	0.90[CEU][hapmap];0.89[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9380586	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[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	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
2	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6902994	SERPINE3	trans	lymphoblastoid	seeQTL
rs6902994	ITPR3	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36609600-36617000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:36611400-36616600	Weak transcription	HUVEC	blood vessel
3	chr6:36611600-36617000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:36611600-36617600	Weak transcription	Lung	lung
5	chr6:36611600-36628600	Weak transcription	Right Atrium	heart
6	chr6:36611800-36616800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:36611800-36617000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:36611800-36617400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:36612000-36617400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:36612000-36617400	Weak transcription	Colonic Mucosa	Colon
11	chr6:36612000-36617400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:36612000-36617400	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:36612000-36617400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:36612000-36617400	Weak transcription	Spleen	Spleen
15	chr6:36612600-36617400	Weak transcription	Fetal Intestine Large	intestine
16	chr6:36612800-36617200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:36613000-36616800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:36613000-36617400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:36613000-36617400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:36613000-36617400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr6:36613000-36617400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:36613000-36617600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:36613200-36616800	Weak transcription	Adipose Nuclei	Adipose
24	chr6:36613200-36617000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:36613200-36617000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:36613200-36617000	Weak transcription	GM12878-XiMat	blood
27	chr6:36613200-36617000	Weak transcription	HSMM	muscle
28	chr6:36613200-36617000	Weak transcription	HSMMtube	muscle
29	chr6:36613200-36617200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr6:36613200-36617400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:36613200-36617400	Weak transcription	HMEC	breast
32	chr6:36613200-36617600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:36613200-36618600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr6:36613200-36619600	Weak transcription	Placenta	Placenta
35	chr6:36613400-36617000	Weak transcription	Osteobl	bone
36	chr6:36613400-36617600	Weak transcription	Hela-S3	cervix
37	chr6:36613400-36625000	Weak transcription	Fetal Kidney	kidney
38	chr6:36613600-36617200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr6:36613600-36618000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:36613800-36617200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr6:36615200-36616000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr6:36615200-36616200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:36615400-36615800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:36615600-36616000	Enhancers	Fetal Intestine Small	intestine
45	chr6:36615600-36616400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:36615600-36616600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:36615600-36617400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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