Variant report

Variant	rs61943399
Chromosome Location	chr12:118831433-118831434
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:118827680..118830142-chr12:118830318..118832919,2	MCF-7	breast:

Extended variants
information (count: 124 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10082823	0.85[EUR][1000 genomes]
rs1060964	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850967	0.86[EUR][1000 genomes]
rs11068917	0.83[EUR][1000 genomes]
rs11068919	0.88[EUR][1000 genomes]
rs11068926	0.92[EUR][1000 genomes]
rs17440669	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17440774	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17440823	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17440893	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17440942	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17440956	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17441033	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17441047	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17441061	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17441075	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17441172	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17441214	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17441251	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512525	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17512574	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17512609	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512644	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17512652	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512763	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17513006	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17513013	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17619932	0.84[EUR][1000 genomes]
rs1909617	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036314	0.91[EUR][1000 genomes]
rs2036489	0.86[EUR][1000 genomes]
rs2055534	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062519	0.86[EUR][1000 genomes]
rs2393403	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393415	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393416	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2893771	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4406856	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4442583	0.92[EUR][1000 genomes]
rs4457791	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766899	0.86[EUR][1000 genomes]
rs4766900	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767671	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767672	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507517	1.00[ASN][1000 genomes]
rs55659011	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55842338	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55929628	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56133316	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56157623	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56190986	1.00[ASN][1000 genomes]
rs56275187	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56284927	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56324376	0.86[EUR][1000 genomes]
rs56347775	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59594854	0.86[EUR][1000 genomes]
rs61943364	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs61943367	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943368	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943369	0.91[EUR][1000 genomes]
rs61943370	0.92[EUR][1000 genomes]
rs61943371	0.92[EUR][1000 genomes]
rs61943385	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943389	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943391	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943392	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943397	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943400	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943401	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943402	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943403	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943404	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943405	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943406	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943443	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943444	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943447	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943451	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943452	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943454	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943455	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943456	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943457	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945192	0.82[AFR][1000 genomes]
rs61945212	0.82[AFR][1000 genomes]
rs61945220	0.82[AFR][1000 genomes]
rs61945221	0.82[AFR][1000 genomes]
rs61946067	0.82[AFR][1000 genomes]
rs61946068	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6490177	0.83[EUR][1000 genomes]
rs7132753	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7136676	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137184	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295288	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299040	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304342	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305647	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307393	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7309484	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309671	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7312555	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7315458	0.84[EUR][1000 genomes]
rs73205531	0.82[AFR][1000 genomes]
rs73205576	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73205579	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73205594	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73207504	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73207564	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73207566	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958551	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7958652	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7967900	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968011	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882927	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884844	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs950288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965524	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv899547	chr12:118791441-118896304	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61943399	SUDS3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118815800-118839600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:118815800-118855200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:118816000-118862000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:118816200-118863400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:118816400-118835600	Strong transcription	Fetal Muscle Leg	muscle
6	chr12:118816400-118838600	Strong transcription	Fetal Stomach	stomach
7	chr12:118816400-118855000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:118816400-118855400	Strong transcription	Fetal Muscle Trunk	muscle
9	chr12:118816800-118831800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:118816800-118839400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:118816800-118841600	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr12:118816800-118844400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr12:118816800-118855000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:118816800-118855200	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:118816800-118855400	Strong transcription	Primary T cells from cord blood	blood
16	chr12:118816800-118856600	Strong transcription	Placenta	Placenta
17	chr12:118817000-118845600	Strong transcription	Duodenum Mucosa	Duodenum
18	chr12:118817000-118846000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:118817000-118855600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:118817000-118856000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr12:118817200-118832600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr12:118817200-118833000	Strong transcription	Fetal Lung	lung
23	chr12:118817200-118834200	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:118817200-118837400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:118817200-118839400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:118817200-118839600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:118817200-118841800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:118817200-118841800	Strong transcription	Fetal Brain Female	brain
29	chr12:118817200-118841800	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:118817200-118842600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:118817200-118845600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:118817200-118845800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:118817200-118848800	Strong transcription	Dnd41	blood
34	chr12:118817200-118850400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:118817200-118854400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:118817200-118854800	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:118817200-118855400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:118817200-118856600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:118817200-118856600	Strong transcription	Fetal Intestine Large	intestine
40	chr12:118817400-118833000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:118817400-118833000	Strong transcription	NH-A	brain
42	chr12:118817400-118833800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:118817400-118835000	Strong transcription	Stomach Smooth Muscle	stomach
44	chr12:118817400-118836000	Strong transcription	Fetal Thymus	thymus
45	chr12:118817400-118841800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:118817400-118842000	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr12:118817400-118842400	Strong transcription	Thymus	Thymus
48	chr12:118817400-118845200	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr12:118817400-118845400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr12:118817400-118849800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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