Variant report

Variant	rs41498747
Chromosome Location	chr1:174914122-174914123
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174909477..174911004-chr1:174913375..174915350,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10489330	0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap]
rs10489332	0.88[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap]
rs11811190	0.80[AFR][1000 genomes]
rs12140378	0.83[CHB][hapmap]
rs12737503	0.80[AFR][1000 genomes]
rs16847730	0.88[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs2861106	0.82[YRI][hapmap]
rs3753562	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41266060	0.80[AFR][1000 genomes]
rs41266064	0.80[AFR][1000 genomes]
rs4565668	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4650666	0.82[YRI][hapmap]
rs57053120	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58762254	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs59436654	0.87[AFR][1000 genomes]
rs60893569	0.84[AFR][1000 genomes]
rs61028529	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6673649	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs6688577	1.00[YRI][hapmap]
rs6692753	1.00[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap]
rs6700434	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv1794782	chr1:174900761-174925112	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41498747	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174874200-174938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:174876800-174933600	Weak transcription	Aorta	Aorta
3	chr1:174899800-174915200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:174901000-174922200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:174908000-174914600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:174908000-174926600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:174908000-174932400	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr1:174908200-174914200	Weak transcription	Small Intestine	intestine
9	chr1:174908200-174914800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:174908200-174915200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:174908200-174924200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:174908600-174927400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:174908800-174932200	Weak transcription	Primary T cells from cord blood	blood
14	chr1:174910000-174916000	Enhancers	Fetal Intestine Large	intestine
15	chr1:174910400-174922400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:174910400-174932400	Weak transcription	HSMMtube	muscle
17	chr1:174910600-174914800	Weak transcription	K562	blood
18	chr1:174910800-174925800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:174910800-174957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:174911400-174915000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:174912200-174918400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:174912200-174925400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:174912400-174914200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:174912400-174914200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:174912400-174914200	Weak transcription	Fetal Lung	lung
26	chr1:174912400-174922400	Weak transcription	Right Atrium	heart
27	chr1:174912400-174922600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:174912400-174923800	Weak transcription	Gastric	stomach
29	chr1:174912600-174914200	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:174912600-174914200	Weak transcription	Brain Substantia Nigra	brain
31	chr1:174912600-174914600	Weak transcription	Stomach Mucosa	stomach
32	chr1:174912600-174914800	Weak transcription	Primary B cells from cord blood	blood
33	chr1:174912600-174914800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:174912600-174914800	Weak transcription	Fetal Kidney	kidney
35	chr1:174912600-174914800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:174912600-174918600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:174912600-174921800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr1:174912600-174922600	Weak transcription	Brain Angular Gyrus	brain
39	chr1:174912600-174923800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:174912600-174934800	Weak transcription	Left Ventricle	heart
41	chr1:174913000-174915400	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr1:174913200-174915000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:174913400-174915800	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:174913800-174914400	Enhancers	Brain Germinal Matrix	brain
45	chr1:174913800-174914800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr1:174913800-174915400	Enhancers	Fetal Heart	heart
47	chr1:174913800-174915400	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr1:174913800-174915800	Enhancers	Fetal Intestine Small	intestine
49	chr1:174913800-174922800	Weak transcription	Pancreas	Pancrea
50	chr1:174914000-174914200	Enhancers	Rectal Mucosa Donor 29	rectum

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