Variant report

Variant	rs1869870
Chromosome Location	chr3:47027482-47027483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:47027289-47027491	MCF-7	breast:	n/a	n/a
2	JUN	chr3:47027090-47030381	K562	blood:	n/a	chr3:47029370-47029379 chr3:47030122-47030131 chr3:47029082-47029091 chr3:47029074-47029083 chr3:47027901-47027915
3	POLR2A	chr3:47027200-47027495	A549	lung:	n/a	n/a
4	NR3C1	chr3:47027472-47027878	A549	lung:	n/a	chr3:47027735-47027752 chr3:47027736-47027750 chr3:47027736-47027750 chr3:47027570-47027583

No.	Distal block	Cell Line	Cell type
1	chr3:46988383..46991103-chr3:47025292..47027507,2	MCF-7	breast:
2	chr3:47026019..47028000-chr3:47321803..47324300,2	K562	blood:
3	chr3:46943427..46945149-chr3:47026537..47029447,2	K562	blood:
4	chr3:46974856..46983636-chr3:47025231..47032249,9	K562	blood:
5	chr3:46953705..46956072-chr3:47026187..47029077,2	K562	blood:

Variant related genes	Relation type
CCDC12	TF binding region
ENSG00000088727	Chromatin interaction
ENSG00000160801	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs10461017	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10461019	0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs11130108	0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130109	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11706212	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11708257	0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709693	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709876	0.85[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11713537	0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs11928558	0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12330516	1.00[EUR][1000 genomes]
rs12487763	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12631730	0.94[YRI][hapmap]
rs13062185	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13062516	0.85[AFR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs13079416	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13082531	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13323092	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs1378818	0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463394	0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466272	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466273	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466274	0.89[AMR][1000 genomes]
rs1473382	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473384	1.00[EUR][1000 genomes]
rs1473385	1.00[EUR][1000 genomes]
rs1563431	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1563432	1.00[EUR][1000 genomes]
rs1814564	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1874264	1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2124509	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2124510	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs2385863	1.00[EUR][1000 genomes]
rs2385868	0.85[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2385869	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28735306	1.00[EUR][1000 genomes]
rs2891887	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2891893	0.86[YRI][hapmap];0.89[AMR][1000 genomes]
rs34147581	1.00[EUR][1000 genomes]
rs35366910	1.00[EUR][1000 genomes]
rs4018904	0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs4282092	0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4289375	0.81[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4324490	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4373094	0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4378998	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4389512	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4450857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4478107	0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4522803	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4525902	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4543047	0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682828	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682832	0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682833	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682834	1.00[EUR][1000 genomes]
rs4682835	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682836	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682838	0.82[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682840	0.89[AMR][1000 genomes]
rs4682841	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682843	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682846	1.00[EUR][1000 genomes]
rs4682847	1.00[EUR][1000 genomes]
rs4683277	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683279	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683282	0.85[YRI][hapmap]
rs4683283	0.83[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683284	0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683285	0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683286	0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683288	1.00[EUR][1000 genomes]
rs4683289	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683290	0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683291	0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683292	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683303	1.00[EUR][1000 genomes]
rs6442041	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442042	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442043	0.82[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442044	0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442047	0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442048	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6766676	0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6768169	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6772449	1.00[EUR][1000 genomes]
rs6775797	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6778687	1.00[EUR][1000 genomes]
rs6780994	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6785462	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787210	1.00[EUR][1000 genomes]
rs6804732	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6806521	0.85[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808052	1.00[EUR][1000 genomes]
rs6808117	1.00[EUR][1000 genomes]
rs6808629	1.00[EUR][1000 genomes]
rs6809904	0.82[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621530	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7624549	0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7625011	0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7630154	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs7630904	0.82[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7638549	0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7639121	1.00[EUR][1000 genomes]
rs7643150	1.00[EUR][1000 genomes]
rs7643868	0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7644382	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs7646076	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs7649413	1.00[EUR][1000 genomes]
rs7649941	0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650142	0.81[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs936173	1.00[EUR][1000 genomes]
rs936177	0.82[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936178	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936179	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936180	0.81[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936181	0.81[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936182	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936185	1.00[EUR][1000 genomes]
rs936186	0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9810881	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9812407	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9819344	1.00[EUR][1000 genomes]
rs9819475	1.00[EUR][1000 genomes]
rs9823480	1.00[EUR][1000 genomes]
rs9826488	1.00[EUR][1000 genomes]
rs9827293	1.00[EUR][1000 genomes]
rs9828473	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs9833500	1.00[EUR][1000 genomes]
rs9836801	1.00[EUR][1000 genomes]
rs9850151	1.00[EUR][1000 genomes]
rs9852167	1.00[EUR][1000 genomes]
rs9861247	1.00[EUR][1000 genomes]
rs9861265	1.00[EUR][1000 genomes]
rs9862711	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869489	1.00[EUR][1000 genomes]
rs9878813	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9883152	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9883909	1.00[EUR][1000 genomes]
rs9990284	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
7	esv1800172	chr3:47013346-47049306	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv590209	chr3:47018214-47050784	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	nsv876757	chr3:47018214-47058057	Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47021800-47028400	Weak transcription	Small Intestine	intestine
2	chr3:47021800-47036000	Weak transcription	Ovary	ovary
3	chr3:47022000-47030200	Weak transcription	Aorta	Aorta
4	chr3:47022200-47030200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:47022400-47028800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:47022400-47029600	Weak transcription	Liver	Liver
7	chr3:47022400-47039800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:47022400-47041600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:47022400-47041800	Weak transcription	Brain Germinal Matrix	brain
10	chr3:47022400-47042000	Weak transcription	Brain Substantia Nigra	brain
11	chr3:47022600-47027800	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr3:47022600-47028200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:47022600-47028200	Weak transcription	Fetal Heart	heart
14	chr3:47022600-47028400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr3:47022600-47028600	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr3:47022600-47028600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:47022600-47049000	Weak transcription	Hela-S3	cervix
18	chr3:47022600-47050600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:47023200-47042000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:47023400-47028400	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:47023600-47028200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr3:47023600-47028200	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:47023600-47028600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr3:47023600-47028800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:47023600-47035600	Weak transcription	Brain Anterior Caudate	brain
26	chr3:47023800-47027600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr3:47023800-47027600	Weak transcription	A549	lung
28	chr3:47023800-47028000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:47023800-47028200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:47023800-47028200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:47023800-47028400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:47023800-47028400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:47023800-47028400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:47023800-47029000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:47023800-47029600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:47024000-47028000	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:47024000-47028400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr3:47024200-47028000	Weak transcription	Adipose Nuclei	Adipose
39	chr3:47024200-47028000	Weak transcription	HUVEC	blood vessel
40	chr3:47024200-47028400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:47024200-47028600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:47024200-47028800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:47024200-47029400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:47024200-47030400	Weak transcription	Fetal Brain Female	brain
45	chr3:47024400-47027800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:47024400-47028400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:47024400-47030000	Enhancers	Stomach Mucosa	stomach
48	chr3:47024400-47039600	Weak transcription	HepG2	liver
49	chr3:47024600-47028600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:47024600-47028600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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