Variant report

Variant	rs3934627
Chromosome Location	chr2:173301379-173301380
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	chr2:173297263..173301573-chr2:173305902..173308346,3	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10171775	0.98[ASN][1000 genomes]
rs10175670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10184567	0.87[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs10195932	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10197251	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10497381	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1076595	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs12465295	0.85[JPT][hapmap]
rs12465442	0.85[JPT][hapmap]
rs12467358	0.85[JPT][hapmap]
rs12469875	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12473999	0.80[ASN][1000 genomes]
rs12477247	0.85[JPT][hapmap]
rs12477594	0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs12478465	0.85[JPT][hapmap]
rs12622044	0.92[ASN][1000 genomes]
rs16860377	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs16860418	0.81[YRI][hapmap]
rs2293646	0.85[JPT][hapmap]
rs2357415	0.85[JPT][hapmap]
rs28464102	0.83[ASN][1000 genomes]
rs28540552	0.87[ASN][1000 genomes]
rs3749148	0.85[JPT][hapmap]
rs3762619	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs3792260	0.85[JPT][hapmap]
rs4281870	0.96[ASN][1000 genomes]
rs4480959	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4993282	0.85[ASN][1000 genomes]
rs4993283	0.85[ASN][1000 genomes]
rs6718477	0.85[JPT][hapmap]
rs6721597	0.84[ASN][1000 genomes]
rs6755100	0.85[JPT][hapmap]
rs7564174	0.81[YRI][hapmap]
rs7567159	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7594126	0.81[YRI][hapmap]
rs7604441	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7608097	0.86[MEX][hapmap];0.83[TSI][hapmap]

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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv875414	chr2:173267081-173307756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1847874	chr2:173277361-173308318	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv583663	chr2:173287832-173307756	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv583664	chr2:173289239-173307756	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3934627	DHRS9	cis	cerebellum	SCAN
rs3934627	PPIG	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173294000-173301800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr2:173294200-173302600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:173294400-173301400	Weak transcription	Aorta	Aorta
4	chr2:173294600-173302400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:173294600-173302600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:173294600-173302600	Weak transcription	NH-A	brain
7	chr2:173294600-173303000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:173294600-173303400	Weak transcription	NHLF	lung
9	chr2:173294800-173302400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:173294800-173302400	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr2:173294800-173306400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:173294800-173308800	Enhancers	Stomach Mucosa	stomach
13	chr2:173295000-173302200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr2:173295000-173303800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:173295200-173302600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:173295200-173306600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr2:173295200-173306600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr2:173295600-173301600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:173295600-173308600	Enhancers	Fetal Intestine Large	intestine
20	chr2:173295800-173302400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr2:173296000-173301800	Weak transcription	HSMM	muscle
22	chr2:173296000-173302400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr2:173296000-173305600	Weak transcription	Fetal Lung	lung
24	chr2:173296000-173307600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr2:173296200-173303800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:173296200-173305000	Enhancers	H9 Cell Line	embryonic stem cell
27	chr2:173296200-173307600	Enhancers	Fetal Thymus	thymus
28	chr2:173296400-173303400	Weak transcription	Liver	Liver
29	chr2:173296600-173308600	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr2:173296800-173302000	Enhancers	Brain Anterior Caudate	brain
31	chr2:173297000-173306600	Enhancers	Small Intestine	intestine
32	chr2:173297000-173307600	Enhancers	Pancreas	Pancrea
33	chr2:173297200-173303400	Enhancers	Thymus	Thymus
34	chr2:173297200-173304800	Weak transcription	Fetal Kidney	kidney
35	chr2:173297400-173301800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:173297400-173303600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:173297400-173304000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:173297600-173307400	Enhancers	Spleen	Spleen
39	chr2:173298400-173302800	Weak transcription	Brain Substantia Nigra	brain
40	chr2:173298600-173302000	Enhancers	Gastric	stomach
41	chr2:173298600-173304000	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr2:173299000-173301600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:173299200-173304000	Enhancers	Right Atrium	heart
44	chr2:173299200-173305000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr2:173299400-173302400	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr2:173299400-173302600	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr2:173299400-173303600	Enhancers	HUVEC	blood vessel
48	chr2:173299600-173302600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:173299800-173302600	Enhancers	HSMMtube	muscle
50	chr2:173299800-173304200	Enhancers	Psoas Muscle	Psoas

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