Variant report

Variant	rs7570877
Chromosome Location	chr2:48743051-48743052
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	chr2:48739322..48741224-chr2:48741836..48744392,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11674217	0.88[CEU][hapmap]
rs11675947	0.90[EUR][1000 genomes]
rs11678934	0.88[CEU][hapmap]
rs11687498	0.92[EUR][1000 genomes]
rs11687771	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs11689285	0.88[CEU][hapmap]
rs11689288	0.86[EUR][1000 genomes]
rs11690526	0.88[CEU][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs11692537	0.88[CEU][hapmap]
rs11693784	0.92[EUR][1000 genomes]
rs13386132	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs2937	0.88[CEU][hapmap]
rs34026270	0.82[EUR][1000 genomes]
rs34542838	0.82[EUR][1000 genomes]
rs3811520	0.92[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs4464333	0.92[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs4952913	0.86[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap]
rs4953590	0.93[ASN][1000 genomes]
rs6545040	0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs7355307	0.82[JPT][hapmap]
rs7577850	1.00[CHB][hapmap];0.94[JPT][hapmap]

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	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7570877	KLRAQ1	cis	parietal	SCAN
rs7570877	CCDC128	Cis_1M	lymphoblastoid	RTeQTL
rs7570877	STON1-GTF2A1L	cis	cerebellum	SCAN
rs7570877	UNQ6975	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48694200-48753000	Weak transcription	Psoas Muscle	Psoas
2	chr2:48709400-48755200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:48710200-48745000	Weak transcription	Fetal Brain Male	brain
4	chr2:48723800-48748200	Strong transcription	GM12878-XiMat	blood
5	chr2:48726400-48756800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:48728200-48756800	Weak transcription	HMEC	breast
7	chr2:48732200-48751400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:48732400-48743400	Strong transcription	Primary hematopoietic stem cells	blood
9	chr2:48732400-48749600	Strong transcription	Primary B cells from cord blood	blood
10	chr2:48736000-48752800	Weak transcription	Small Intestine	intestine
11	chr2:48736200-48749400	Strong transcription	Primary B cells from peripheral blood	blood
12	chr2:48736200-48749400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:48736400-48748400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:48736400-48749600	Strong transcription	Liver	Liver
15	chr2:48736400-48750000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:48736400-48752600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:48736400-48753400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:48736400-48754600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:48736600-48746600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:48736600-48749600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:48736600-48749800	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr2:48736800-48747200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:48736800-48749400	Strong transcription	Fetal Thymus	thymus
24	chr2:48736800-48749600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr2:48737000-48744400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:48737000-48748200	Strong transcription	Duodenum Mucosa	Duodenum
27	chr2:48737000-48748600	Strong transcription	Dnd41	blood
28	chr2:48737000-48749600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:48737000-48749600	Strong transcription	Brain Anterior Caudate	brain
30	chr2:48737200-48750600	Strong transcription	Fetal Intestine Large	intestine
31	chr2:48737400-48747000	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr2:48737600-48744800	Strong transcription	HepG2	liver
33	chr2:48737600-48747000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:48737600-48749800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:48737600-48750200	Strong transcription	Primary T cells from cord blood	blood
36	chr2:48737800-48749400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr2:48737800-48750000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:48737800-48752000	Strong transcription	Fetal Intestine Small	intestine
39	chr2:48737800-48756200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:48738000-48749600	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:48738000-48750000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:48738000-48755400	Weak transcription	HUVEC	blood vessel
43	chr2:48738000-48756800	Weak transcription	NH-A	brain
44	chr2:48738200-48746800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:48738200-48753800	Weak transcription	Hela-S3	cervix
46	chr2:48738400-48744000	Strong transcription	Brain Hippocampus Middle	brain
47	chr2:48738400-48745600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:48739200-48744200	Weak transcription	HSMM	muscle
49	chr2:48739400-48746000	Strong transcription	A549	lung
50	chr2:48739800-48744600	Weak transcription	Lung	lung

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