Variant report

Variant	rs943478
Chromosome Location	chr6:33750940-33750941
allele	A/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	chr6:33750133-33750978	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr6:33750866-33751304	HepG2	liver:	n/a	n/a
3	NRF1	chr6:33750864-33751043	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33750065..33752378-chr6:33760799..33763522,2	MCF-7	breast:
2	chr6:33746735..33748851-chr6:33749721..33751563,2	MCF-7	breast:

Variant related genes	Relation type
LEMD2	TF binding region
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12173787	0.88[EUR][1000 genomes]
rs12190029	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2013365	0.90[AFR][1000 genomes]
rs2281820	0.89[EUR][1000 genomes]
rs2296744	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2296746	0.81[AFR][1000 genomes]
rs2296747	0.93[AFR][1000 genomes]
rs2296748	0.81[AFR][1000 genomes]
rs2395402	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711347	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4711348	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4711349	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4711355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713678	0.80[EUR][1000 genomes]
rs4713679	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4713681	0.93[AFR][1000 genomes]
rs6457741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6922275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6929696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs747694	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs751728	0.88[AFR][1000 genomes]
rs7774620	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9357164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380378	0.89[AFR][1000 genomes]
rs9394166	0.81[AFR][1000 genomes]
rs9394167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs943471	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs943474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs943475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs943479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33738600-33753200	Strong transcription	Thymus	Thymus
2	chr6:33739600-33752600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:33739600-33754000	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:33739800-33752400	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr6:33739800-33752600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:33739800-33753000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr6:33739800-33753000	Strong transcription	Primary T cells from cord blood	blood
8	chr6:33739800-33753000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:33739800-33753600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:33740000-33752400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr6:33740000-33752600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:33740000-33752600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:33740000-33752800	Strong transcription	Dnd41	blood
14	chr6:33740000-33753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:33740000-33753000	Strong transcription	HepG2	liver
16	chr6:33740000-33753200	Strong transcription	Primary hematopoietic stem cells	blood
17	chr6:33740000-33753600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr6:33740000-33753600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr6:33740200-33751600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:33740200-33751800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:33740200-33752400	Strong transcription	Rectal Smooth Muscle	rectum
22	chr6:33740200-33752600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
23	chr6:33740200-33753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:33740200-33753400	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr6:33740200-33754000	Strong transcription	Primary B cells from cord blood	blood
26	chr6:33740400-33752600	Strong transcription	Colon Smooth Muscle	Colon
27	chr6:33740400-33752800	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr6:33740400-33753200	Strong transcription	Aorta	Aorta
29	chr6:33740400-33753600	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:33740600-33753000	Strong transcription	Liver	Liver
31	chr6:33740600-33753000	Strong transcription	Colonic Mucosa	Colon
32	chr6:33740600-33754200	Strong transcription	Fetal Intestine Large	intestine
33	chr6:33740600-33754200	Strong transcription	Fetal Intestine Small	intestine
34	chr6:33741000-33751600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr6:33741000-33752600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr6:33741000-33753000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr6:33741000-33753200	Strong transcription	Fetal Brain Female	brain
38	chr6:33741000-33754000	Strong transcription	Fetal Thymus	thymus
39	chr6:33741400-33753000	Strong transcription	Fetal Lung	lung
40	chr6:33741400-33753000	Strong transcription	Ovary	ovary
41	chr6:33741400-33753200	Strong transcription	Fetal Stomach	stomach
42	chr6:33741600-33751600	Strong transcription	Stomach Smooth Muscle	stomach
43	chr6:33741800-33752600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:33741800-33752800	Strong transcription	Fetal Kidney	kidney
45	chr6:33742400-33752000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
46	chr6:33742400-33752800	Strong transcription	Small Intestine	intestine
47	chr6:33743200-33753200	Strong transcription	GM12878-XiMat	blood
48	chr6:33744200-33754400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:33744600-33752000	Strong transcription	Brain Cingulate Gyrus	brain
50	chr6:33744600-33753000	Strong transcription	Brain Substantia Nigra	brain

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