Variant report

Variant	rs2146341
Chromosome Location	chr6:11196817-11196818
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	RXRA	chr6:11196474-11197082	SK-N-SH	brain:	n/a	chr6:11196746-11196755
2	TCF12	chr6:11196773-11196953	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr6:11196544-11197214	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr6:11196536-11197208	SK-N-SH	brain:	n/a	chr6:11196748-11196758
5	RCOR1	chr6:11196464-11197868	IMR90	lung:	n/a	n/a
6	ZBTB33	chr6:11196521-11197032	SK-N-SH	brain:	n/a	n/a
7	TEAD4	chr6:11196643-11197185	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr6:11196424-11199925	HepG2	liver:	n/a	n/a
9	PBX3	chr6:11196545-11197189	SK-N-SH	brain:	n/a	chr6:11197135-11197155
10	GATA3	chr6:11196453-11197832	SK-N-SH	brain:	n/a	chr6:11196748-11196758 chr6:11197461-11197471
11	FOSL2	chr6:11196544-11197135	SK-N-SH	brain:	n/a	chr6:11196929-11196938
12	EP300	chr6:11196661-11196997	SK-N-SH_RA	brain:	n/a	chr6:11196784-11196798 chr6:11196921-11196937
13	POLR2A	chr6:11194225-11199844	HepG2	liver:	n/a	n/a
14	MAZ	chr6:11196492-11198146	IMR90	lung:	n/a	chr6:11196927-11196937
15	EP300	chr6:11196484-11197902	SK-N-SH	brain:	n/a	chr6:11197459-11197473 chr6:11197479-11197489 chr6:11196784-11196798 chr6:11196921-11196937
16	REST	chr6:11196607-11196973	SK-N-SH	brain:	n/a	chr6:11196921-11196931
17	PBX3	chr6:11196528-11197109	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr6:11196563-11199803	HepG2	liver:	n/a	n/a
19	POLR2A	chr6:11196704-11198544	IMR90	lung:	n/a	n/a
20	FOSL2	chr6:11196440-11199678	HepG2	liver:	n/a	chr6:11197857-11197868 chr6:11198018-11198025 chr6:11197461-11197470 chr6:11196929-11196938
21	POLR2A	chr6:11196690-11196851	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr6:11196524-11199784	A549	lung:	n/a	n/a
23	POLR2A	chr6:11196805-11197308	HepG2	liver:	n/a	n/a
24	TCF12	chr6:11196687-11197044	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr6:11196561-11197098	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr6:11193180-11197406	HepG2	liver:	n/a	n/a
27	MAX	chr6:11196618-11197062	SK-N-SH	brain:	n/a	chr6:11196927-11196937
28	TCF12	chr6:11196470-11197626	SK-N-SH	brain:	n/a	n/a
29	EP300	chr6:11196645-11196971	SK-N-SH_RA	brain:	n/a	chr6:11196784-11196798 chr6:11196921-11196937
30	NFIC	chr6:11196474-11197211	SK-N-SH	brain:	n/a	n/a
31	HEY1	chr6:11196463-11198922	HepG2	liver:	n/a	n/a
32	TCF12	chr6:11196497-11197224	SK-N-SH	brain:	n/a	n/a
33	MAFK	chr6:11196663-11197636	IMR90	lung:	n/a	chr6:11197177-11197193 chr6:11197178-11197189 chr6:11197177-11197188 chr6:11197176-11197190 chr6:11197300-11197311 chr6:11197178-11197189 chr6:11197177-11197188 chr6:11197178-11197198 chr6:11197180-11197196 chr6:11197177-11197192

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11142606..11145240-chr6:11195647..11197361,2	K562	blood:
2	chr6:11194955..11197803-chr6:11232255..11234030,2	MCF-7	breast:

Variant related genes	Relation type
NEDD9	TF binding region
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1465131	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1885662	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2025677	0.80[CEU][hapmap]
rs2078599	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4053067	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4711193	0.89[CEU][hapmap]
rs4713247	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs6456970	0.91[CEU][hapmap]
rs6457107	0.80[CEU][hapmap]
rs9368610	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs941982	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs943007	0.81[CEU][hapmap]

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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11179000-11202200	Weak transcription	Brain Substantia Nigra	brain
2	chr6:11183000-11199000	Strong transcription	Primary B cells from peripheral blood	blood
3	chr6:11184400-11197000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:11185800-11202600	Weak transcription	Brain Angular Gyrus	brain
5	chr6:11186800-11200400	Weak transcription	HMEC	breast
6	chr6:11189000-11197000	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr6:11190400-11198800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:11190800-11201400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:11191000-11198600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:11191000-11199000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:11191000-11200200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:11191200-11197200	Weak transcription	Brain Anterior Caudate	brain
13	chr6:11191200-11200400	Weak transcription	NHEK	skin
14	chr6:11191800-11197400	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:11191800-11201400	Weak transcription	Esophagus	oesophagus
16	chr6:11192000-11198000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:11192000-11198600	Weak transcription	Spleen	Spleen
18	chr6:11192000-11199000	Weak transcription	Pancreas	Pancrea
19	chr6:11192000-11202600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:11192200-11198000	Weak transcription	Fetal Brain Female	brain
21	chr6:11192200-11198800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr6:11192400-11197000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr6:11192400-11199000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:11192600-11198600	Weak transcription	Small Intestine	intestine
25	chr6:11192600-11199000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:11192800-11202800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:11192800-11207000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr6:11192800-11207200	Weak transcription	Liver	Liver
29	chr6:11193000-11199000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr6:11194000-11198400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr6:11194000-11199600	Enhancers	Fetal Heart	heart
32	chr6:11194000-11200200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:11194000-11200200	Weak transcription	Fetal Intestine Large	intestine
34	chr6:11194000-11200400	Weak transcription	Colonic Mucosa	Colon
35	chr6:11194000-11202200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:11194000-11202600	Weak transcription	Brain Germinal Matrix	brain
37	chr6:11194200-11198200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr6:11194200-11199200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:11194400-11197000	Enhancers	NHDF-Ad	bronchial
40	chr6:11194400-11198600	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr6:11194400-11199600	Enhancers	Adipose Nuclei	Adipose
42	chr6:11194600-11197000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr6:11194600-11198600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr6:11194600-11198800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr6:11194600-11199000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr6:11194800-11197000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:11194800-11197000	Enhancers	HSMM	muscle
48	chr6:11194800-11197000	Enhancers	HSMMtube	muscle
49	chr6:11194800-11197800	Weak transcription	Primary B cells from cord blood	blood
50	chr6:11194800-11198400	Enhancers	H1 Cell Line	embryonic stem cell

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