Variant report

Variant	rs1138454
Chromosome Location	chr3:17208267-17208268
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	chr3:17207202..17210072-chr3:17213126..17214686,2	MCF-7	breast:
2	chr3:17203436..17206201-chr3:17208117..17210640,2	MCF-7	breast:

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1463220	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470346	0.84[CEU][hapmap];0.80[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs2470584	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4337625	0.81[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	nsv1008636	chr3:17173415-17208267	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1138454	GALNTL2	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17191400-17217600	Weak transcription	Small Intestine	intestine
2	chr3:17192200-17211400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:17193400-17210000	Strong transcription	Fetal Intestine Large	intestine
4	chr3:17194000-17211400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:17194800-17210400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:17195000-17224200	Weak transcription	Fetal Kidney	kidney
7	chr3:17195200-17223000	Weak transcription	Fetal Brain Female	brain
8	chr3:17195400-17209600	Strong transcription	Dnd41	blood
9	chr3:17195600-17208400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:17195600-17209600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:17195600-17210000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:17195600-17210800	Strong transcription	Stomach Smooth Muscle	stomach
13	chr3:17195800-17219000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr3:17196000-17209800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr3:17196200-17208600	Strong transcription	Primary B cells from cord blood	blood
16	chr3:17196200-17209600	Strong transcription	Liver	Liver
17	chr3:17196200-17210200	Strong transcription	Adipose Nuclei	Adipose
18	chr3:17196600-17212200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:17196800-17209800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:17197000-17210800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:17197200-17210200	Strong transcription	Spleen	Spleen
22	chr3:17197200-17211200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:17197400-17209600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr3:17197600-17209600	Strong transcription	Lung	lung
25	chr3:17198400-17225200	Weak transcription	HMEC	breast
26	chr3:17198600-17208400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:17198600-17210600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:17198600-17212600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:17199800-17208400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:17200000-17209200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr3:17200200-17209200	Strong transcription	Placenta	Placenta
32	chr3:17200200-17209600	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:17200200-17216800	Weak transcription	HSMMtube	muscle
34	chr3:17200400-17216400	Weak transcription	NHDF-Ad	bronchial
35	chr3:17200400-17216600	Weak transcription	NH-A	brain
36	chr3:17200600-17210000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:17200800-17225600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:17201000-17208600	Strong transcription	Fetal Thymus	thymus
39	chr3:17201000-17216400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr3:17201000-17220400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:17201200-17236200	Weak transcription	Fetal Brain Male	brain
42	chr3:17201800-17209000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:17202000-17209600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:17202200-17213000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:17202400-17216400	Weak transcription	HSMM	muscle
46	chr3:17202400-17217200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:17202600-17212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr3:17202800-17209000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr3:17202800-17217400	Weak transcription	HUVEC	blood vessel
50	chr3:17203000-17209000	Strong transcription	Brain Substantia Nigra	brain

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