Variant report

Variant	rs17882441
Chromosome Location	chr11:102187213-102187214
allele	A/G
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	RELA	chr11:102187107-102189859	GM12891	blood:	n/a	chr11:102188016-102188025 chr11:102188016-102188025
2	TBP	chr11:102186993-102188850	Hela-S3	cervix:	n/a	n/a
3	RUNX3	chr11:102187185-102188779	GM12878	blood:	n/a	n/a
4	CUX1	chr11:102187011-102189668	GM12878	blood:	n/a	chr11:102188785-102188794
5	POLR2A	chr11:102186906-102189937	GM12878	blood:	n/a	n/a
6	POLR2A	chr11:102186912-102189926	GM12892	blood:	n/a	n/a
7	POLR2A	chr11:102186826-102190807	MCF10A-Er-Src	breast:	n/a	n/a
8	CHD1	chr11:102187037-102189800	GM12878	blood:	n/a	n/a
9	TCF7L2	chr11:102187051-102188720	PANC-1	pancreas:	n/a	chr11:102187488-102187504 chr11:102187293-102187307 chr11:102187490-102187500 chr11:102187296-102187305 chr11:102187489-102187503 chr11:102187491-102187500 chr11:102187292-102187308 chr11:102187492-102187501 chr11:102187488-102187504 chr11:102187292-102187308
10	RELA	chr11:102187188-102189755	GM18951	blood:	n/a	chr11:102188016-102188025 chr11:102188016-102188025
11	STAT3	chr11:102187100-102187254	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr11:102186986-102187546	GM12891	blood:	n/a	n/a
13	RUNX3	chr11:102187093-102187551	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:102187053-102189739	GM12878	blood:	n/a	n/a
15	POLR2A	chr11:102186922-102190829	GM12892	blood:	n/a	n/a
16	POLR2A	chr11:102187106-102187540	GM12891	blood:	n/a	n/a
17	TBP	chr11:102186940-102189636	GM12878	blood:	n/a	n/a
18	POLR2A	chr11:102186917-102187510	GM12892	blood:	n/a	n/a
19	POLR2A	chr11:102187051-102187525	GM12891	blood:	n/a	n/a
20	POLR2A	chr11:102187114-102189846	Raji	blood:	n/a	n/a
21	TCF7L2	chr11:102187174-102188762	Hela-S3	cervix:	n/a	chr11:102187488-102187504 chr11:102187293-102187307 chr11:102187490-102187500 chr11:102187296-102187305 chr11:102187489-102187503 chr11:102187491-102187500 chr11:102187292-102187308 chr11:102187492-102187501 chr11:102187488-102187504 chr11:102187292-102187308
22	NFIC	chr11:102187152-102188663	GM12878	blood:	n/a	n/a
23	MTA3	chr11:102187022-102187574	GM12878	blood:	n/a	n/a
24	WRNIP1	chr11:102187084-102187440	GM12878	blood:	n/a	n/a
25	POLR2A	chr11:102187146-102190780	GM18951	blood:	n/a	n/a
26	POLR2A	chr11:102186834-102189826	GM12878	blood:	n/a	n/a
27	POLR2A	chr11:102186992-102187563	PANC-1	pancreas:	n/a	n/a
28	STAT3	chr11:102187010-102188323	GM12878	blood:	n/a	chr11:102187587-102187594 chr11:102187750-102187761
29	GATA2	chr11:102187103-102187547	SH-SY5Y	brain:	n/a	n/a
30	POLR2A	chr11:102186998-102191851	GM19099	blood:	n/a	n/a
31	NFIC	chr11:102186943-102189830	GM12878	blood:	n/a	n/a
32	MTA3	chr11:102186989-102189858	GM12878	blood:	n/a	n/a
33	PML	chr11:102187161-102189819	GM12878	blood:	n/a	n/a
34	POLR2A	chr11:102186998-102189891	GM12878	blood:	n/a	n/a
35	GATA3	chr11:102187186-102187462	SH-SY5Y	brain:	n/a	n/a
36	POLR2A	chr11:102187073-102189767	GM12892	blood:	n/a	n/a
37	RELA	chr11:102187194-102189619	GM10847	blood:	n/a	chr11:102188016-102188025 chr11:102188016-102188025
38	POLR2A	chr11:102187041-102191957	GM18505	blood:	n/a	n/a
39	RELA	chr11:102187015-102189759	GM18505	blood:	n/a	chr11:102188016-102188025 chr11:102188016-102188025
40	POLR2A	chr11:102186808-102192224	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr11:102186909-102191988	GM12891	blood:	n/a	n/a
42	POLR2A	chr11:102187031-102187513	GM12891	blood:	n/a	n/a
43	POLR2A	chr11:102186935-102187611	GM12892	blood:	n/a	n/a
44	RELA	chr11:102186976-102189734	GM19099	blood:	n/a	chr11:102188016-102188025 chr11:102188016-102188025
45	RELA	chr11:102187100-102189736	GM12878	blood:	n/a	chr11:102188016-102188025 chr11:102188016-102188025
46	BRCA1	chr11:102187125-102188965	Hela-S3	cervix:	n/a	n/a
47	MXI1	chr11:102187183-102189803	GM12878	blood:	n/a	n/a
48	POLR2A	chr11:102187186-102189484	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr11:102186664-102199529	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:102175561..102178536-chr11:102186960..102189576,2	MCF-7	breast:
2	chr11:102186736..102188260-chr11:102321581..102323426,2	K562	blood:
3	chr11:102183249..102185212-chr11:102186159..102188587,3	K562	blood:
4	chr11:102176632..102179702-chr11:102185117..102189773,6	MCF-7	breast:
5	chr11:102187104..102190463-chr11:102217868..102220185,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM123-3	chr11:102186657-102187303	NONHSAT023874
2	lnc-TMEM123-3	chr11:102186657-102187303	FPKM1_group_5225_transcript_1

Variant related genes	Relation type
BIRC3	TF binding region
ENSG00000212466	Chromatin interaction
ENSG00000110330	Chromatin interaction
ENSG00000271600	Chromatin interaction
ENSG00000152558	Chromatin interaction
ENSG00000270868	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17880156	1.00[AFR][1000 genomes]
rs17882391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2155587	0.91[CEU][hapmap]
rs61895367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052348	chr11:101987090-102255753	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv556141	chr11:101988061-102207851	Weak transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1050961	chr11:101993880-102253717	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1051735	chr11:101993880-102255753	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv530646	chr11:102000840-102238992	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv3514195	chr11:102118479-102348362	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv3514197	chr11:102118479-102348362	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102176800-102187800	Weak transcription	Pancreas	Pancrea
2	chr11:102177000-102187800	Weak transcription	Spleen	Spleen
3	chr11:102178200-102188000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:102178400-102187800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:102184200-102187400	Weak transcription	Psoas Muscle	Psoas
6	chr11:102184200-102187800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:102184200-102187800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr11:102184200-102187800	Weak transcription	Left Ventricle	heart
9	chr11:102184200-102187800	Weak transcription	K562	blood
10	chr11:102184200-102188000	Weak transcription	Lung	lung
11	chr11:102184200-102188200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr11:102184400-102187800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:102184400-102187800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:102184400-102187800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:102184400-102187800	Weak transcription	Placenta	Placenta
16	chr11:102184400-102187800	Weak transcription	HUVEC	blood vessel
17	chr11:102184600-102187400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:102184600-102187600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:102184600-102187600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:102184600-102187600	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr11:102184600-102187600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:102184600-102187600	Weak transcription	Aorta	Aorta
23	chr11:102184600-102187600	Weak transcription	Right Atrium	heart
24	chr11:102184600-102187600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr11:102184600-102187800	Weak transcription	Brain Angular Gyrus	brain
26	chr11:102184600-102187800	Weak transcription	Brain Hippocampus Middle	brain
27	chr11:102184600-102187800	Weak transcription	Fetal Kidney	kidney
28	chr11:102184600-102187800	Weak transcription	NH-A	brain
29	chr11:102184800-102187800	Weak transcription	Brain Germinal Matrix	brain
30	chr11:102184800-102187800	Weak transcription	Fetal Heart	heart
31	chr11:102184800-102187800	Weak transcription	Fetal Lung	lung
32	chr11:102185000-102187400	Weak transcription	HSMM	muscle
33	chr11:102185000-102187800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr11:102185000-102187800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:102185600-102187800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:102185600-102187800	Weak transcription	Small Intestine	intestine
37	chr11:102185800-102187800	Weak transcription	Liver	Liver
38	chr11:102186400-102187400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr11:102186800-102187600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr11:102186800-102187600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr11:102187000-102187400	Enhancers	Primary hematopoietic stem cells	blood
42	chr11:102187000-102187400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr11:102187000-102187400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr11:102187000-102187400	Flanking Active TSS	A549	lung
45	chr11:102187000-102187400	Flanking Active TSS	GM12878-XiMat	blood
46	chr11:102187000-102187400	Enhancers	HepG2	liver
47	chr11:102187000-102187600	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr11:102187000-102187600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr11:102187000-102187600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr11:102187000-102187600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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