Variant report

Variant	rs73139941
Chromosome Location	chr7:66236128-66236129
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66233619..66236445-chr7:66238794..66241787,2	MCF-7	breast:

Extended variants
information (count: 119 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10224536	0.86[EUR][1000 genomes]
rs10225392	0.85[EUR][1000 genomes]
rs10226191	0.81[AFR][1000 genomes]
rs10228381	0.81[EUR][1000 genomes]
rs10229580	0.85[EUR][1000 genomes]
rs10231411	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10231860	0.87[EUR][1000 genomes]
rs10234322	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10234747	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10235037	0.87[EUR][1000 genomes]
rs10235638	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10237244	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10240153	0.85[EUR][1000 genomes]
rs10240582	0.85[EUR][1000 genomes]
rs10241395	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10241528	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10242870	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10243608	0.88[EUR][1000 genomes]
rs10244459	0.88[EUR][1000 genomes]
rs10247324	0.84[EUR][1000 genomes]
rs10250124	0.84[AMR][1000 genomes]
rs10252133	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10256117	0.86[EUR][1000 genomes]
rs10257393	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10258628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10262184	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10263993	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10264223	0.82[AFR][1000 genomes]
rs10265069	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10265154	0.84[EUR][1000 genomes]
rs10266041	0.84[EUR][1000 genomes]
rs10267253	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10267834	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10270326	0.86[EUR][1000 genomes]
rs10271177	0.85[EUR][1000 genomes]
rs10273320	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10275343	0.82[AFR][1000 genomes]
rs10277231	0.84[EUR][1000 genomes]
rs10278343	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10278763	0.81[EUR][1000 genomes]
rs10280431	0.86[EUR][1000 genomes]
rs10281090	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10281544	0.84[EUR][1000 genomes]
rs10281734	0.87[EUR][1000 genomes]
rs10282310	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10282522	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10479728	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1060527	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1064795	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12234826	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12333749	0.85[EUR][1000 genomes]
rs12334214	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13437901	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13438432	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17138208	0.87[EUR][1000 genomes]
rs17138274	0.85[EUR][1000 genomes]
rs1882656	0.84[EUR][1000 genomes]
rs1882657	0.83[EUR][1000 genomes]
rs2013707	0.81[EUR][1000 genomes]
rs28368585	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28375318	0.87[EUR][1000 genomes]
rs28379824	0.85[EUR][1000 genomes]
rs28460006	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28526115	0.81[EUR][1000 genomes]
rs28533332	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28547918	0.83[EUR][1000 genomes]
rs28560293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28607736	0.86[EUR][1000 genomes]
rs28615327	0.85[EUR][1000 genomes]
rs28634091	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs28657758	0.81[EUR][1000 genomes]
rs28663128	0.83[EUR][1000 genomes]
rs28729561	0.82[AFR][1000 genomes]
rs3757419	0.85[EUR][1000 genomes]
rs3764904	0.84[EUR][1000 genomes]
rs3778907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778908	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3800814	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3823607	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3823609	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3962133	0.88[EUR][1000 genomes]
rs4518552	0.81[EUR][1000 genomes]
rs4718417	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56743740	0.82[AFR][1000 genomes]
rs57774708	0.81[AFR][1000 genomes]
rs57902746	0.84[EUR][1000 genomes]
rs59079543	0.84[EUR][1000 genomes]
rs60026498	0.81[AFR][1000 genomes]
rs60972148	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61093354	0.84[EUR][1000 genomes]
rs61700307	0.84[EUR][1000 genomes]
rs67408913	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6964080	0.84[EUR][1000 genomes]
rs6973897	0.85[EUR][1000 genomes]
rs6974601	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73133851	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73133859	0.84[EUR][1000 genomes]
rs73133865	0.84[EUR][1000 genomes]
rs73135905	0.84[EUR][1000 genomes]
rs73135907	0.84[EUR][1000 genomes]
rs73135909	0.84[EUR][1000 genomes]
rs73135917	0.84[EUR][1000 genomes]
rs73135922	0.84[EUR][1000 genomes]
rs73135925	0.84[EUR][1000 genomes]
rs73135950	0.84[EUR][1000 genomes]
rs73135960	0.85[EUR][1000 genomes]
rs73135973	0.83[EUR][1000 genomes]
rs73137960	0.86[EUR][1000 genomes]
rs73137963	0.83[EUR][1000 genomes]
rs73141980	0.81[AFR][1000 genomes]
rs73143998	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7455757	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7777631	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7796977	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9654843	0.84[EUR][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	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv981512	chr7:66223352-66249901	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs73139941	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx
rs73139941	GS1-124K5.12	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66206800-66238800	Weak transcription	Aorta	Aorta
2	chr7:66207000-66238400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr7:66207000-66238400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr7:66207000-66255200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr7:66207600-66239800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr7:66208000-66236800	Weak transcription	Dnd41	blood
7	chr7:66208000-66238000	Weak transcription	A549	lung
8	chr7:66208000-66238600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:66208000-66238600	Weak transcription	Brain Germinal Matrix	brain
10	chr7:66208000-66240800	Weak transcription	HSMMtube	muscle
11	chr7:66208000-66241800	Weak transcription	Hela-S3	cervix
12	chr7:66209400-66239000	Weak transcription	HMEC	breast
13	chr7:66212000-66236800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:66214400-66236600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:66214400-66239400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr7:66216800-66239400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr7:66220000-66241000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr7:66221800-66240400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:66223600-66237600	Weak transcription	Liver	Liver
20	chr7:66223800-66236800	Weak transcription	Spleen	Spleen
21	chr7:66223800-66238400	Weak transcription	Lung	lung
22	chr7:66224200-66238200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr7:66224400-66237000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr7:66224400-66238400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr7:66224400-66238600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:66224800-66237000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:66226400-66238400	Weak transcription	Fetal Muscle Leg	muscle
28	chr7:66227000-66243000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr7:66227600-66238600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:66228800-66236800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:66229200-66239200	Weak transcription	Fetal Lung	lung
32	chr7:66229800-66238800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr7:66230800-66238400	Weak transcription	HUVEC	blood vessel
34	chr7:66231000-66236800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr7:66231000-66237000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr7:66231000-66239000	Weak transcription	NH-A	brain
37	chr7:66231200-66237400	Weak transcription	Stomach Mucosa	stomach
38	chr7:66231200-66238200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr7:66231200-66246400	Weak transcription	Right Ventricle	heart
40	chr7:66231400-66237000	Weak transcription	Fetal Intestine Large	intestine
41	chr7:66231400-66237000	Weak transcription	HepG2	liver
42	chr7:66231400-66238200	Weak transcription	Psoas Muscle	Psoas
43	chr7:66231400-66255000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr7:66232600-66279800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:66232800-66236600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr7:66232800-66238200	Weak transcription	Esophagus	oesophagus
47	chr7:66232800-66238400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr7:66232800-66238400	Weak transcription	Left Ventricle	heart
49	chr7:66233000-66241600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr7:66233200-66239600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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