Variant report

Variant	rs7773780
Chromosome Location	chr6:145955442-145955443
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:145817967..145818790-chr6:145955063..145955734,2	MCF-7	breast:
2	chr6:145535549..145536107-chr6:145954859..145955499,2	MCF-7	breast:
3	chr6:145812363..145812895-chr6:145954847..145955707,2	MCF-7	breast:

Extended variants
information (count: 136 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs12111090	0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12111476	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1591698	0.90[AFR][1000 genomes]
rs28479261	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs28587324	0.90[AFR][1000 genomes]
rs28829296	0.90[AFR][1000 genomes]
rs4896845	0.80[AFR][1000 genomes]
rs4896847	0.80[AFR][1000 genomes]
rs55658016	0.90[AFR][1000 genomes]
rs55746945	0.90[AFR][1000 genomes]
rs55813779	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs55814547	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs55820518	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs56116838	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs56198487	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs56282473	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs56864636	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs56950953	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs57105639	0.90[AFR][1000 genomes]
rs57472392	0.82[AMR][1000 genomes]
rs57646957	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs58588227	0.86[AFR][1000 genomes]
rs59135568	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs59557516	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs60162832	0.81[AFR][1000 genomes]
rs60609437	0.81[AFR][1000 genomes]
rs61014905	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs61041405	0.93[AFR][1000 genomes]
rs61121433	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6570702	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6570704	0.85[YRI][hapmap];0.91[AMR][1000 genomes]
rs6570707	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6570709	0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6570710	0.90[AFR][1000 genomes]
rs6570714	0.82[AFR][1000 genomes]
rs6570720	0.89[YRI][hapmap]
rs6900158	0.88[AFR][1000 genomes]
rs6901219	0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs6901587	0.81[AFR][1000 genomes]
rs6902273	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6902358	0.81[AFR][1000 genomes]
rs6902952	0.89[YRI][hapmap];0.95[AFR][1000 genomes]
rs6904060	0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[AMR][1000 genomes]
rs6908707	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6913497	0.93[YRI][hapmap];0.95[AFR][1000 genomes]
rs6914491	0.82[YRI][hapmap];0.89[AFR][1000 genomes]
rs6914746	0.81[LWK][hapmap]
rs6918350	0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6918739	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6919173	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6920248	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs6921110	0.88[AFR][1000 genomes]
rs6921551	0.81[LWK][hapmap]
rs6925420	0.91[AMR][1000 genomes]
rs6927960	0.90[AFR][1000 genomes]
rs6928780	0.90[AFR][1000 genomes]
rs6930335	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs6931280	0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs6938028	0.81[LWK][hapmap]
rs6938895	0.81[LWK][hapmap]
rs6940415	0.95[AFR][1000 genomes]
rs6940752	0.91[AMR][1000 genomes]
rs6940930	0.85[YRI][hapmap];0.91[AMR][1000 genomes]
rs73562628	0.91[AMR][1000 genomes]
rs73564486	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73566113	0.87[AFR][1000 genomes]
rs73566115	0.90[AFR][1000 genomes]
rs73566121	0.90[AFR][1000 genomes]
rs73566126	0.90[AFR][1000 genomes]
rs73566139	0.88[AFR][1000 genomes]
rs73566140	0.88[AFR][1000 genomes]
rs73566157	0.87[AFR][1000 genomes]
rs73566168	0.87[AFR][1000 genomes]
rs73566721	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73566724	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73566728	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73566742	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73566747	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73566751	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73566754	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73566757	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73568127	0.86[AFR][1000 genomes]
rs73568130	0.87[AFR][1000 genomes]
rs73568133	0.87[AFR][1000 genomes]
rs73568134	0.87[AFR][1000 genomes]
rs73568138	0.86[AFR][1000 genomes]
rs73568145	0.82[AFR][1000 genomes]
rs73568148	0.82[AFR][1000 genomes]
rs73568151	0.82[AFR][1000 genomes]
rs73568362	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73568366	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73568375	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73568383	0.91[AMR][1000 genomes]
rs73568384	0.91[AMR][1000 genomes]
rs73568389	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73568402	0.91[AMR][1000 genomes]
rs73577358	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73577363	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73577384	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73579444	0.91[AMR][1000 genomes]
rs73579478	0.92[AFR][1000 genomes]
rs73579483	0.94[AFR][1000 genomes]
rs73579498	0.95[AFR][1000 genomes]
rs73782053	0.95[AFR][1000 genomes]
rs73782068	0.87[AFR][1000 genomes]
rs73784038	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73784067	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7738406	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7738822	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7738906	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7741139	0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs7744082	0.89[YRI][hapmap];0.95[AFR][1000 genomes]
rs7745379	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs7745722	0.94[AFR][1000 genomes]
rs7749377	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7750382	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7751866	0.91[AMR][1000 genomes]
rs7753694	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7753832	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs7754367	0.87[AFR][1000 genomes]
rs7756614	0.89[MKK][hapmap]
rs7757137	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7758839	0.95[AFR][1000 genomes]
rs7759254	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7761251	0.87[AFR][1000 genomes]
rs7761577	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs7763273	0.88[AFR][1000 genomes]
rs7768195	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7771112	0.83[AFR][1000 genomes]
rs7771653	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7772012	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7772550	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9718033	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9766595	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9766596	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933782	chr6:145946431-145956458	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145946400-145955600	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:145947000-145955800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:145948800-145962400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:145949000-145956200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:145949000-145968000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:145949200-145955600	Weak transcription	Fetal Thymus	thymus
7	chr6:145950400-145955600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:145950800-145955600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:145950800-145977400	Weak transcription	Aorta	Aorta
10	chr6:145950800-145990600	Weak transcription	Primary B cells from cord blood	blood
11	chr6:145951000-145959000	Weak transcription	Fetal Intestine Small	intestine
12	chr6:145951000-146003000	Weak transcription	Thymus	Thymus
13	chr6:145951200-145955800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:145951400-146003000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:145952200-145983200	Weak transcription	Primary T cells from cord blood	blood
16	chr6:145952600-145955800	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr6:145953400-145955600	Enhancers	Left Ventricle	heart
18	chr6:145953600-145958600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:145953800-145955600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr6:145954600-145955600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr6:145954600-145955600	Enhancers	Stomach Smooth Muscle	stomach
22	chr6:145954600-145955800	Enhancers	Fetal Heart	heart
23	chr6:145955000-145955600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:145955000-145955600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:145955000-145955600	Enhancers	Liver	Liver
26	chr6:145955000-145955600	Enhancers	Rectal Smooth Muscle	rectum
27	chr6:145955000-145955600	Enhancers	Stomach Mucosa	stomach
28	chr6:145955000-145955800	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr6:145955000-145962400	Weak transcription	Psoas Muscle	Psoas
30	chr6:145955200-145955800	Enhancers	Brain Anterior Caudate	brain
31	chr6:145955200-145976800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:145955400-145955600	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr6:145955400-145955600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:145955400-145955600	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr6:145955400-145955600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:145955400-145955600	Enhancers	Primary B cells from peripheral blood	blood
37	chr6:145955400-145955600	Enhancers	Primary T cells fromperipheralblood	blood
38	chr6:145955400-145955600	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr6:145955400-145955600	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr6:145955400-145955600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:145955400-145955600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:145955400-145955600	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr6:145955400-145955600	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr6:145955400-145955600	Enhancers	Brain Hippocampus Middle	brain
45	chr6:145955400-145955600	Enhancers	Brain Substantia Nigra	brain
46	chr6:145955400-145955600	Enhancers	Esophagus	oesophagus
47	chr6:145955400-145955600	Enhancers	Fetal Muscle Leg	muscle
48	chr6:145955400-145955600	Enhancers	Lung	lung
49	chr6:145955400-145955600	Enhancers	Ovary	ovary
50	chr6:145955400-145955600	Enhancers	Pancreas	Pancrea

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