Variant report

Variant	rs1677141
Chromosome Location	chr12:21786118-21786119
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:21784403..21786252-chr12:21800427..21803138,2	K562	blood:
2	chr12:21785349..21786145-chr16:82057494..82058055,2	HCT-116	colon:
3	chr12:21785834..21786377-chr2:165477655..165478232,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000115290	Chromatin interaction

Extended variants
information (count: 176 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:170)

rs_ID	r²[population]
rs1012354	1.00[EUR][1000 genomes]
rs1030452	1.00[EUR][1000 genomes]
rs1030453	1.00[EUR][1000 genomes]
rs1072992	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs1072993	1.00[EUR][1000 genomes]
rs10841863	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10841864	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10841865	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10841866	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11829561	1.00[EUR][1000 genomes]
rs11835091	1.00[EUR][1000 genomes]
rs1427830	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1478293	1.00[EUR][1000 genomes]
rs1540405	1.00[EUR][1000 genomes]
rs1614040	1.00[EUR][1000 genomes]
rs1616390	1.00[EUR][1000 genomes]
rs1624003	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1626167	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1626303	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1629683	1.00[EUR][1000 genomes]
rs1630514	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1650271	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1650272	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1650277	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1650278	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1650279	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1650280	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1650282	1.00[EUR][1000 genomes]
rs1650283	0.80[AFR][1000 genomes]
rs1650284	0.87[AFR][1000 genomes]
rs1650285	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1650286	1.00[EUR][1000 genomes]
rs1650287	1.00[EUR][1000 genomes]
rs1650288	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1650289	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs1650290	1.00[EUR][1000 genomes]
rs1650291	1.00[EUR][1000 genomes]
rs1650292	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1650293	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs1650294	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1650295	1.00[EUR][1000 genomes]
rs1650297	1.00[EUR][1000 genomes]
rs1650300	1.00[EUR][1000 genomes]
rs1650301	1.00[EUR][1000 genomes]
rs1650305	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs1650306	1.00[EUR][1000 genomes]
rs1650310	1.00[EUR][1000 genomes]
rs1650312	1.00[EUR][1000 genomes]
rs1650314	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs1650315	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs1650318	1.00[EUR][1000 genomes]
rs1677073	1.00[EUR][1000 genomes]
rs1677074	1.00[EUR][1000 genomes]
rs1677078	1.00[EUR][1000 genomes]
rs1677079	1.00[EUR][1000 genomes]
rs1677085	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs1677088	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1677090	0.86[ASW][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1677092	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1677093	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1677094	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1677095	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1677096	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1677097	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1677098	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1677100	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1677104	1.00[EUR][1000 genomes]
rs1677105	1.00[EUR][1000 genomes]
rs1677106	1.00[EUR][1000 genomes]
rs1677107	1.00[EUR][1000 genomes]
rs1677109	1.00[EUR][1000 genomes]
rs1677110	1.00[EUR][1000 genomes]
rs1677111	1.00[EUR][1000 genomes]
rs1677113	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1677118	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1677124	0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1677125	1.00[EUR][1000 genomes]
rs1677126	1.00[EUR][1000 genomes]
rs1677127	1.00[EUR][1000 genomes]
rs1677128	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1677129	0.86[ASW][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs1677131	1.00[EUR][1000 genomes]
rs1677132	1.00[EUR][1000 genomes]
rs1677133	1.00[EUR][1000 genomes]
rs1677134	0.86[ASW][hapmap];0.94[MKK][hapmap]
rs1677135	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1677136	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1677138	1.00[EUR][1000 genomes]
rs1677139	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1677140	0.86[AFR][1000 genomes]
rs1813751	1.00[EUR][1000 genomes]
rs2077044	1.00[EUR][1000 genomes]
rs2217238	1.00[EUR][1000 genomes]
rs255445	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs255449	1.00[EUR][1000 genomes]
rs255452	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2559823	0.93[AFR][1000 genomes]
rs2617117	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2617118	0.96[AFR][1000 genomes]
rs4237915	1.00[EUR][1000 genomes]
rs4438091	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4762714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4762716	1.00[EUR][1000 genomes]
rs4762856	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4762858	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4762859	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4762862	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56013787	1.00[EUR][1000 genomes]
rs56035640	1.00[EUR][1000 genomes]
rs56066637	1.00[EUR][1000 genomes]
rs56160727	1.00[EUR][1000 genomes]
rs56271252	1.00[EUR][1000 genomes]
rs56729740	1.00[EUR][1000 genomes]
rs56871137	1.00[EUR][1000 genomes]
rs56994698	1.00[EUR][1000 genomes]
rs57115374	1.00[EUR][1000 genomes]
rs57200111	1.00[EUR][1000 genomes]
rs57338327	1.00[EUR][1000 genomes]
rs57842305	1.00[EUR][1000 genomes]
rs58465040	1.00[EUR][1000 genomes]
rs58527132	1.00[EUR][1000 genomes]
rs59247664	1.00[EUR][1000 genomes]
rs59468844	1.00[EUR][1000 genomes]
rs59541120	1.00[EUR][1000 genomes]
rs60486179	1.00[EUR][1000 genomes]
rs60632805	1.00[EUR][1000 genomes]
rs60652753	1.00[EUR][1000 genomes]
rs61187969	1.00[EUR][1000 genomes]
rs61410104	0.85[AFR][1000 genomes]
rs61482461	1.00[EUR][1000 genomes]
rs7135799	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs7299671	0.85[AFR][1000 genomes]
rs7299674	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7299680	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7300051	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73249228	1.00[EUR][1000 genomes]
rs73249231	1.00[EUR][1000 genomes]
rs73249234	1.00[EUR][1000 genomes]
rs73249241	1.00[EUR][1000 genomes]
rs73249265	1.00[EUR][1000 genomes]
rs73249266	1.00[EUR][1000 genomes]
rs73249268	1.00[EUR][1000 genomes]
rs73249276	1.00[EUR][1000 genomes]
rs73249282	1.00[EUR][1000 genomes]
rs73262386	1.00[EUR][1000 genomes]
rs736047	1.00[EUR][1000 genomes]
rs74066770	1.00[EUR][1000 genomes]
rs74067628	1.00[EUR][1000 genomes]
rs74069327	1.00[EUR][1000 genomes]
rs74069332	1.00[EUR][1000 genomes]
rs74069333	1.00[EUR][1000 genomes]
rs74069343	1.00[EUR][1000 genomes]
rs74069345	1.00[EUR][1000 genomes]
rs74069349	1.00[EUR][1000 genomes]
rs74069350	1.00[EUR][1000 genomes]
rs74069351	1.00[EUR][1000 genomes]
rs74069352	1.00[EUR][1000 genomes]
rs74069353	1.00[EUR][1000 genomes]
rs74069354	1.00[EUR][1000 genomes]
rs74069355	1.00[EUR][1000 genomes]
rs74069356	1.00[EUR][1000 genomes]
rs74069357	1.00[EUR][1000 genomes]
rs74069362	1.00[EUR][1000 genomes]
rs74069363	1.00[EUR][1000 genomes]
rs759931	1.00[EUR][1000 genomes]
rs759932	1.00[EUR][1000 genomes]
rs759933	0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs759934	1.00[EUR][1000 genomes]
rs7974267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs962947	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats 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	nsv1036084	chr12:21631009-21792756	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv469164	chr12:21688900-21966701	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv557744	chr12:21688900-21966701	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv832349	chr12:21749093-21930695	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21769400-21786600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:21773200-21786800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:21777600-21786200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:21778800-21787000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:21779000-21786800	Weak transcription	Ovary	ovary
6	chr12:21779600-21787200	Weak transcription	Brain Angular Gyrus	brain
7	chr12:21780400-21787000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:21780600-21786200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:21780600-21786800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:21780800-21786200	Weak transcription	Fetal Stomach	stomach
11	chr12:21781200-21786200	Weak transcription	Fetal Intestine Small	intestine
12	chr12:21781200-21786200	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:21781200-21787000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:21781200-21787200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:21781200-21787200	Weak transcription	Esophagus	oesophagus
16	chr12:21781200-21787200	Weak transcription	Pancreas	Pancrea
17	chr12:21781200-21787200	Weak transcription	Psoas Muscle	Psoas
18	chr12:21781200-21788200	Weak transcription	Right Ventricle	heart
19	chr12:21781200-21796400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:21781200-21809600	Weak transcription	Small Intestine	intestine
21	chr12:21781600-21787200	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:21781800-21786200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:21781800-21787000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:21781800-21787200	Weak transcription	Spleen	Spleen
25	chr12:21782000-21786200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:21782000-21786400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr12:21782000-21787200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:21782000-21790600	Weak transcription	Fetal Heart	heart
29	chr12:21782200-21791000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr12:21782600-21787000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr12:21782600-21787200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr12:21782600-21805400	Weak transcription	Colonic Mucosa	Colon
33	chr12:21783000-21787200	Weak transcription	Brain Germinal Matrix	brain
34	chr12:21783600-21786200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr12:21783600-21787200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:21783800-21787200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr12:21783800-21801600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:21784000-21786400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:21784000-21789800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr12:21784000-21791000	Weak transcription	Fetal Brain Male	brain
41	chr12:21784200-21786800	Weak transcription	Lung	lung
42	chr12:21784200-21787200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr12:21784200-21789000	Strong transcription	Primary T cells from cord blood	blood
44	chr12:21784400-21786200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:21784400-21786800	Weak transcription	Adipose Nuclei	Adipose
46	chr12:21784400-21787200	Weak transcription	HSMM	muscle
47	chr12:21784600-21786200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:21784600-21786800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr12:21784600-21786800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:21784600-21786800	Weak transcription	Fetal Muscle Trunk	muscle

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