Variant report

Variant	rs3087749
Chromosome Location	chr7:4780514-4780515
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:4779354..4780876-chr7:4813776..4815968,2	K562	blood:
2	chr7:4778391..4781100-chr7:4828582..4831115,2	K562	blood:
3	chr7:4777828..4782067-chr7:4812094..4815733,5	K562	blood:
4	chr7:4718155..4726493-chr7:4775257..4787798,22	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242802	Chromatin interaction
ENSG00000164916	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10228886	0.96[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.81[MKK][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10232008	0.82[ASN][1000 genomes]
rs10257680	0.86[ASN][1000 genomes]
rs10261971	0.92[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10277273	0.81[ASN][1000 genomes]
rs11765781	0.86[JPT][hapmap]
rs12701913	0.84[ASN][1000 genomes]
rs13228233	0.86[JPT][hapmap]
rs13232425	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4077986	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4523152	0.86[JPT][hapmap]
rs4540325	0.86[JPT][hapmap]
rs4720401	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs4720402	0.92[CEU][hapmap]
rs4724033	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6463014	0.81[ASN][1000 genomes]
rs6944865	0.92[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs6946034	0.81[EUR][1000 genomes]
rs6950090	0.81[EUR][1000 genomes]
rs6973046	0.96[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6975499	0.81[ASN][1000 genomes]
rs7781115	0.81[ASN][1000 genomes]
rs7781456	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7784748	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs7786525	0.83[ASN][1000 genomes]
rs7793919	0.88[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529538	chr7:4509189-5151503	Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv887377	chr7:4730535-4862259	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv887378	chr7:4730535-4929721	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv887379	chr7:4749527-4828593	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv887380	chr7:4760124-4929721	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv471293	chr7:4764861-4885221	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv887381	chr7:4769030-4880954	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3087749	RAC1	cis	parietal	SCAN
rs3087749	ZNF12	cis	parietal	SCAN
rs3087749	PAPOLB	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:4765600-4783200	Weak transcription	Fetal Brain Male	brain
2	chr7:4765600-4784000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:4765800-4782400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:4766000-4783600	Weak transcription	HMEC	breast
5	chr7:4768000-4781600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr7:4778800-4780600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr7:4778800-4782200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:4778800-4782400	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr7:4779000-4780600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr7:4779000-4781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:4779200-4781400	Weak transcription	Fetal Brain Female	brain
12	chr7:4779400-4780600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr7:4779400-4781200	Weak transcription	GM12878-XiMat	blood
14	chr7:4779400-4782600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:4779400-4783200	Weak transcription	Psoas Muscle	Psoas
16	chr7:4779600-4780600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:4779600-4780600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:4779600-4780600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:4779600-4780600	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr7:4779600-4780600	Weak transcription	Liver	Liver
21	chr7:4779600-4780600	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:4779600-4780600	Weak transcription	Osteobl	bone
23	chr7:4779600-4780800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:4779600-4781200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr7:4779600-4781200	Weak transcription	Brain Substantia Nigra	brain
26	chr7:4779600-4781200	Weak transcription	Ovary	ovary
27	chr7:4779600-4781200	Weak transcription	Stomach Mucosa	stomach
28	chr7:4779600-4781400	Weak transcription	Brain Angular Gyrus	brain
29	chr7:4779600-4781400	Weak transcription	Brain Anterior Caudate	brain
30	chr7:4779600-4781400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr7:4779600-4781400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr7:4779600-4781400	Strong transcription	Fetal Intestine Small	intestine
33	chr7:4779600-4781400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr7:4779600-4781400	Weak transcription	HSMMtube	muscle
35	chr7:4779600-4781400	Weak transcription	K562	blood
36	chr7:4779600-4781600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr7:4779600-4781600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr7:4779600-4781600	Weak transcription	Fetal Lung	lung
39	chr7:4779600-4781800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr7:4779600-4781800	Weak transcription	NH-A	brain
41	chr7:4779600-4782200	Weak transcription	Fetal Kidney	kidney
42	chr7:4779600-4782600	Weak transcription	HSMM	muscle
43	chr7:4779600-4782800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr7:4779600-4783200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr7:4779600-4783200	Weak transcription	Right Atrium	heart
46	chr7:4779600-4783400	Weak transcription	Small Intestine	intestine
47	chr7:4779600-4783800	Weak transcription	NHDF-Ad	bronchial
48	chr7:4779600-4785400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr7:4779800-4780600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr7:4779800-4780600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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