Variant report

Variant	rs10017177
Chromosome Location	chr4:8404232-8404233
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	chr4:8401612..8405935-chr4:8442501..8444816,3	MCF-7	breast:
2	chr4:8268593..8269552-chr4:8403907..8405561,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155275	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10016221	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1006113	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10938710	0.85[ASN][1000 genomes]
rs10938712	0.97[ASN][1000 genomes]
rs11721377	0.97[ASN][1000 genomes]
rs11724408	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11731308	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11931965	0.96[ASN][1000 genomes]
rs11934603	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11938364	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13103946	0.96[ASN][1000 genomes]
rs13107329	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13130336	0.97[ASN][1000 genomes]
rs13134272	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13136987	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13139522	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13150818	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1568692	0.96[ASN][1000 genomes]
rs1568693	0.96[ASN][1000 genomes]
rs2242483	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2293229	0.99[ASN][1000 genomes]
rs28637781	0.96[ASN][1000 genomes]
rs28805000	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34947973	0.97[ASN][1000 genomes]
rs35893558	0.97[ASN][1000 genomes]
rs3796740	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4543095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447868	0.97[ASN][1000 genomes]
rs73087705	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7668735	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7696306	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9291391	0.94[ASN][1000 genomes]
rs9291392	0.93[ASN][1000 genomes]
rs950306	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv878609	chr4:8373832-8407406	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv878610	chr4:8377058-8416976	ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv470014	chr4:8390646-8429817	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv593639	chr4:8394376-8424108	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10017177	RP11-689P11.2	cis	Artery Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8366400-8411600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr4:8383800-8419000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:8384800-8418600	Strong transcription	Primary T cells from cord blood	blood
4	chr4:8385200-8411600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr4:8385600-8407000	Weak transcription	Stomach Mucosa	stomach
6	chr4:8386400-8408400	Strong transcription	Fetal Intestine Large	intestine
7	chr4:8387400-8412000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr4:8389800-8411400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:8391200-8406400	Weak transcription	Fetal Thymus	thymus
10	chr4:8394200-8407400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:8394800-8409400	Weak transcription	Small Intestine	intestine
12	chr4:8395800-8411800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:8396400-8404800	Weak transcription	A549	lung
14	chr4:8396400-8405800	Weak transcription	GM12878-XiMat	blood
15	chr4:8396600-8404400	Weak transcription	Fetal Kidney	kidney
16	chr4:8396600-8407200	Weak transcription	Dnd41	blood
17	chr4:8396600-8419400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:8396800-8412400	Weak transcription	Fetal Brain Male	brain
19	chr4:8396800-8415600	Weak transcription	NH-A	brain
20	chr4:8397000-8406600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:8397600-8404400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:8397600-8404400	Weak transcription	Fetal Lung	lung
23	chr4:8397600-8409400	Weak transcription	HepG2	liver
24	chr4:8397600-8420400	Weak transcription	NHDF-Ad	bronchial
25	chr4:8397800-8406600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr4:8398000-8406000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr4:8398200-8409400	Weak transcription	Primary B cells from cord blood	blood
28	chr4:8399000-8407000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:8399200-8412000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:8399400-8411800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:8399400-8412000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:8399600-8406400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:8399600-8407200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr4:8399600-8407200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:8399600-8412000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:8399600-8429400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr4:8401200-8405400	Weak transcription	Brain Anterior Caudate	brain
38	chr4:8401200-8406200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr4:8401400-8404400	Weak transcription	Liver	Liver
40	chr4:8401400-8404600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:8401400-8405200	Weak transcription	HSMMtube	muscle
42	chr4:8401400-8405400	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:8401400-8405800	Weak transcription	Ovary	ovary
44	chr4:8401400-8406200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:8401400-8406400	Weak transcription	Gastric	stomach
46	chr4:8401400-8407000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:8401600-8404600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:8401600-8405200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr4:8401600-8405600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr4:8401600-8405800	Weak transcription	Duodenum Mucosa	Duodenum

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