Variant report

Variant	rs4865104
Chromosome Location	chr4:57338551-57338552
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57333435..57335762-chr4:57336689..57342030,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174780	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10007967	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10009543	0.98[ASN][1000 genomes]
rs10015221	0.98[ASN][1000 genomes]
rs10015634	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10518	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10866433	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12646703	0.81[AFR][1000 genomes]
rs12648503	0.88[EUR][1000 genomes]
rs1356787	0.81[AFR][1000 genomes]
rs17086793	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17086803	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086883	0.88[EUR][1000 genomes]
rs17086887	0.88[EUR][1000 genomes]
rs28472763	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4073691	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4383672	0.81[AFR][1000 genomes]
rs4524447	0.81[AFR][1000 genomes]
rs4615235	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4616819	0.81[AFR][1000 genomes]
rs4865102	0.98[ASN][1000 genomes]
rs4865105	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4865110	0.88[EUR][1000 genomes]
rs57523479	0.88[EUR][1000 genomes]
rs58975286	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6584	0.81[AFR][1000 genomes]
rs66599079	0.88[EUR][1000 genomes]
rs68101565	0.88[EUR][1000 genomes]
rs6811482	0.88[EUR][1000 genomes]
rs6811821	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6816218	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6816268	0.81[AFR][1000 genomes]
rs6818715	0.82[AFR][1000 genomes]
rs6819534	0.83[ASN][1000 genomes]
rs6820417	0.84[EUR][1000 genomes]
rs6830518	0.81[AFR][1000 genomes]
rs6832168	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6842307	0.81[AFR][1000 genomes]
rs6843587	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6848187	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7670198	0.88[EUR][1000 genomes]
rs7692073	0.95[ASN][1000 genomes]
rs7694047	0.98[ASN][1000 genomes]
rs7700034	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9312675	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4865104	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57334800-57340200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:57334800-57340200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:57334800-57340200	Weak transcription	Left Ventricle	heart
4	chr4:57334800-57340200	Weak transcription	Small Intestine	intestine
5	chr4:57334800-57340200	Weak transcription	Spleen	Spleen
6	chr4:57334800-57353400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:57334800-57364000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:57334800-57371200	Weak transcription	Stomach Mucosa	stomach
9	chr4:57335000-57340200	Weak transcription	Aorta	Aorta
10	chr4:57335000-57340800	Weak transcription	Colonic Mucosa	Colon
11	chr4:57335000-57354400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:57335200-57340200	Weak transcription	Psoas Muscle	Psoas
13	chr4:57335200-57340200	Weak transcription	Right Ventricle	heart
14	chr4:57335200-57371400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:57335400-57338600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:57335600-57340200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:57335600-57370200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:57335800-57354800	Weak transcription	Fetal Heart	heart
19	chr4:57335800-57359000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:57335800-57365600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:57335800-57369200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:57335800-57370200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:57335800-57370800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:57336000-57339200	Strong transcription	A549	lung
25	chr4:57336000-57340400	Strong transcription	K562	blood
26	chr4:57336000-57342200	Strong transcription	NH-A	brain
27	chr4:57336000-57347600	Strong transcription	Stomach Smooth Muscle	stomach
28	chr4:57336000-57350000	Strong transcription	NHEK	skin
29	chr4:57336000-57362200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr4:57336000-57362600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:57336000-57364200	Strong transcription	Osteobl	bone
32	chr4:57336000-57369400	Strong transcription	Liver	Liver
33	chr4:57336000-57369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:57336000-57370000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:57336000-57370000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr4:57336000-57370200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr4:57336000-57371000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:57336200-57340800	Strong transcription	Fetal Kidney	kidney
39	chr4:57336200-57340800	Strong transcription	HMEC	breast
40	chr4:57336200-57346200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:57336200-57365000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr4:57336200-57369200	Strong transcription	Fetal Thymus	thymus
43	chr4:57336200-57370000	Strong transcription	Placenta	Placenta
44	chr4:57336200-57370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:57336400-57338800	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr4:57336400-57340200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr4:57336400-57342400	Strong transcription	Fetal Intestine Small	intestine
48	chr4:57336400-57342600	Strong transcription	Fetal Stomach	stomach
49	chr4:57336400-57342800	Strong transcription	Brain Germinal Matrix	brain
50	chr4:57336400-57345600	Strong transcription	HUVEC	blood vessel

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