Variant report

Variant	rs10850967
Chromosome Location	chr12:118817877-118817878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:118812421..118814755-chr12:118815512..118818028,2	MCF-7	breast:
2	chr12:118809522..118812617-chr12:118817842..118821161,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135090	Chromatin interaction
ENSG00000111707	Chromatin interaction
ENSG00000270482	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10082823	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10507286	0.85[CEU][hapmap]
rs1060964	1.00[CEU][hapmap]
rs11068891	0.93[CEU][hapmap]
rs11068905	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs11068908	0.93[CEU][hapmap]
rs11068910	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11068917	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs11068919	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11068926	0.94[EUR][1000 genomes]
rs12229607	0.93[CEU][hapmap]
rs12308475	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16948193	0.92[CEU][hapmap]
rs16948197	0.93[CEU][hapmap]
rs16948204	0.93[CEU][hapmap]
rs16948230	0.86[CEU][hapmap]
rs16948234	0.93[CEU][hapmap]
rs16948250	1.00[CEU][hapmap]
rs17440364	0.85[CEU][hapmap]
rs17440433	0.85[CEU][hapmap]
rs17440669	1.00[CEU][hapmap]
rs17440774	1.00[CEU][hapmap]
rs17440823	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs17440893	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17440942	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17440956	1.00[CEU][hapmap]
rs17441033	0.92[CEU][hapmap]
rs17441061	1.00[CEU][hapmap]
rs17441075	0.93[CEU][hapmap]
rs17512142	0.85[CEU][hapmap]
rs17512177	0.84[CEU][hapmap]
rs17512198	0.85[CEU][hapmap]
rs17512219	0.86[CEU][hapmap]
rs17512407	0.93[CEU][hapmap]
rs17512483	1.00[CEU][hapmap]
rs17512525	1.00[CEU][hapmap]
rs17512574	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs17512609	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs17512644	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17512652	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17512763	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17619932	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs1909617	0.86[EUR][1000 genomes]
rs2036314	0.95[EUR][1000 genomes]
rs2036489	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2055534	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2062519	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2280711	0.85[CEU][hapmap]
rs2784	1.00[CEU][hapmap]
rs4442583	0.94[EUR][1000 genomes]
rs4766899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766900	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4767669	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4767670	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4767671	1.00[CEU][hapmap]
rs4767672	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs56133316	0.86[EUR][1000 genomes]
rs56157623	0.86[EUR][1000 genomes]
rs56284927	0.81[EUR][1000 genomes]
rs56324376	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59594854	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943365	0.82[EUR][1000 genomes]
rs61943367	0.86[EUR][1000 genomes]
rs61943368	0.86[EUR][1000 genomes]
rs61943369	0.95[EUR][1000 genomes]
rs61943370	0.94[EUR][1000 genomes]
rs61943371	0.94[EUR][1000 genomes]
rs61943385	0.86[EUR][1000 genomes]
rs61943388	0.86[EUR][1000 genomes]
rs61943389	0.86[EUR][1000 genomes]
rs61943391	0.85[EUR][1000 genomes]
rs61943392	0.86[EUR][1000 genomes]
rs61943393	0.86[EUR][1000 genomes]
rs61943397	0.87[EUR][1000 genomes]
rs61943399	0.86[EUR][1000 genomes]
rs61943400	0.86[EUR][1000 genomes]
rs61943401	0.86[EUR][1000 genomes]
rs61943402	0.86[EUR][1000 genomes]
rs61943403	0.87[EUR][1000 genomes]
rs61943404	0.86[EUR][1000 genomes]
rs61946063	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6490173	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs6490175	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6490177	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7136676	1.00[CEU][hapmap]
rs7137055	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7137184	0.86[EUR][1000 genomes]
rs7294498	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7295288	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7296214	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7299040	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7302387	0.92[CEU][hapmap]
rs7303417	0.93[CEU][hapmap]
rs7304342	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7305647	1.00[CEU][hapmap]
rs7307393	1.00[CEU][hapmap]
rs7309484	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7309671	1.00[CEU][hapmap]
rs7312555	1.00[CEU][hapmap]
rs7314987	0.93[CEU][hapmap]
rs7315458	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73205551	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73205576	0.86[EUR][1000 genomes]
rs73205594	0.86[EUR][1000 genomes]
rs7957828	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7961312	0.93[CEU][hapmap]
rs7962185	0.93[CEU][hapmap]
rs7965350	0.93[CEU][hapmap]
rs7967900	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs7968011	0.86[EUR][1000 genomes]
rs7968371	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7974718	0.80[CEU][hapmap]
rs884844	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs950288	0.86[EUR][1000 genomes]
rs965524	1.00[CEU][hapmap]
rs9943819	0.93[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[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
rs10850967	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	chr12:118815800-118818200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:118815800-118819400	Weak transcription	Gastric	stomach
3	chr12:118815800-118824400	Weak transcription	Stomach Mucosa	stomach
4	chr12:118815800-118827400	Weak transcription	Psoas Muscle	Psoas
5	chr12:118815800-118839600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:118815800-118855200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:118816000-118819400	Weak transcription	Fetal Kidney	kidney
8	chr12:118816000-118862000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:118816200-118819600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:118816200-118819600	Weak transcription	NHEK	skin
11	chr12:118816200-118820800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:118816200-118821000	Weak transcription	HSMM	muscle
13	chr12:118816200-118823200	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:118816200-118823200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:118816200-118824000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:118816200-118824000	Weak transcription	Small Intestine	intestine
17	chr12:118816200-118863400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:118816400-118835600	Strong transcription	Fetal Muscle Leg	muscle
19	chr12:118816400-118838600	Strong transcription	Fetal Stomach	stomach
20	chr12:118816400-118855000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:118816400-118855400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr12:118816600-118818400	Weak transcription	Brain Germinal Matrix	brain
23	chr12:118816600-118818800	Strong transcription	Esophagus	oesophagus
24	chr12:118816600-118820600	Strong transcription	Fetal Intestine Small	intestine
25	chr12:118816800-118818800	Strong transcription	Brain Hippocampus Middle	brain
26	chr12:118816800-118820200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:118816800-118820400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:118816800-118821000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:118816800-118821200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:118816800-118828800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:118816800-118831800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:118816800-118839400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:118816800-118841600	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr12:118816800-118844400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr12:118816800-118855000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:118816800-118855200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr12:118816800-118855400	Strong transcription	Primary T cells from cord blood	blood
38	chr12:118816800-118856600	Strong transcription	Placenta	Placenta
39	chr12:118817000-118819600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:118817000-118820600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:118817000-118821600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:118817000-118845600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr12:118817000-118846000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:118817000-118855600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:118817000-118856000	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr12:118817200-118818600	Strong transcription	HUVEC	blood vessel
47	chr12:118817200-118818800	Strong transcription	Primary B cells from cord blood	blood
48	chr12:118817200-118820000	Strong transcription	Brain Substantia Nigra	brain
49	chr12:118817200-118820200	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:118817200-118820200	Strong transcription	Spleen	Spleen

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