Variant report

Variant	rs11855646
Chromosome Location	chr15:57178528-57178529
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:57176057..57187872-chr15:57206946..57217524,36	K562	blood:
2	chr15:57178056..57181492-chr15:57182204..57185235,4	MCF-7	breast:
3	chr15:57177826..57180634-chr15:57614648..57617463,2	K562	blood:
4	chr15:57178290..57182491-chr15:57208958..57213003,14	K562	blood:
5	chr15:57178055..57182351-chr15:57208260..57213543,21	MCF-7	breast:
6	chr15:57178054..57181022-chr15:57209016..57212878,5	MCF-7	breast:
7	chr15:57169281..57172339-chr15:57176856..57178790,3	K562	blood:
8	chr15:56536601..56538445-chr15:57177718..57180315,2	K562	blood:
9	chr15:57178197..57180890-chr6:86114463..86117112,2	MCF-7	breast:
10	chr15:57173403..57176748-chr15:57177855..57180719,3	MCF-7	breast:
11	chr15:56773647..56776313-chr15:57177229..57179430,2	K562	blood:
12	chr15:57175109..57176620-chr15:57178319..57180528,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MNS1-3	chr15:57178368-57180122	ENSG00000248500

No data

Variant related genes	Relation type
ENSG00000137871	Chromatin interaction
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1012321	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10450961	0.84[EUR][1000 genomes]
rs10851612	0.80[EUR][1000 genomes]
rs11858368	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13379960	0.87[EUR][1000 genomes]
rs1430819	0.86[EUR][1000 genomes]
rs1441236	0.89[EUR][1000 genomes]
rs1647392	0.87[EUR][1000 genomes]
rs1660961	0.83[EUR][1000 genomes]
rs1967352	0.80[EUR][1000 genomes]
rs1967353	0.80[EUR][1000 genomes]
rs2161933	0.86[EUR][1000 genomes]
rs2163369	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2278613	0.80[EUR][1000 genomes]
rs2414487	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28371400	0.96[EUR][1000 genomes]
rs28468978	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28568712	0.87[EUR][1000 genomes]
rs28609621	0.87[EUR][1000 genomes]
rs28736360	0.87[EUR][1000 genomes]
rs28874022	0.89[EUR][1000 genomes]
rs4313751	0.86[EUR][1000 genomes]
rs56965085	0.80[EUR][1000 genomes]
rs6493893	0.85[EUR][1000 genomes]
rs6493894	0.88[EUR][1000 genomes]
rs67114210	0.85[EUR][1000 genomes]
rs67278720	0.85[EUR][1000 genomes]
rs67622899	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68083905	0.83[EUR][1000 genomes]
rs7163302	0.86[EUR][1000 genomes]
rs7167847	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7175191	0.85[EUR][1000 genomes]
rs72747165	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8026149	0.85[EUR][1000 genomes]
rs8040866	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8042606	0.80[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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv833020	chr15:57055947-57216068	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv457162	chr15:57083006-57225766	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv569577	chr15:57083006-57225766	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11855646	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57164800-57178600	Weak transcription	Brain Hippocampus Middle	brain
2	chr15:57169200-57178600	Weak transcription	Fetal Lung	lung
3	chr15:57177000-57178800	Enhancers	Fetal Heart	heart
4	chr15:57177400-57179000	Enhancers	Fetal Thymus	thymus
5	chr15:57177600-57178600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:57177600-57178600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:57177600-57178600	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr15:57177800-57178600	Enhancers	Primary hematopoietic stem cells	blood
9	chr15:57177800-57178600	Enhancers	K562	blood
10	chr15:57177800-57178800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr15:57177800-57178800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr15:57177800-57178800	Enhancers	Primary B cells from cord blood	blood
13	chr15:57177800-57178800	Enhancers	Primary B cells from peripheral blood	blood
14	chr15:57177800-57178800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:57177800-57179000	Enhancers	Spleen	Spleen
16	chr15:57178000-57178600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr15:57178000-57178600	Enhancers	HepG2	liver
18	chr15:57178000-57178800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr15:57178000-57178800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr15:57178000-57178800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr15:57178000-57178800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:57178000-57178800	Enhancers	Fetal Muscle Leg	muscle
23	chr15:57178000-57179000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:57178000-57179000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr15:57178200-57178600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr15:57178200-57178600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr15:57178200-57178600	Enhancers	Brain Angular Gyrus	brain
28	chr15:57178200-57178600	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr15:57178200-57178800	Enhancers	Primary T cells from cord blood	blood
30	chr15:57178200-57178800	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr15:57178200-57178800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr15:57178200-57178800	Enhancers	Fetal Brain Male	brain
33	chr15:57178200-57178800	Enhancers	Dnd41	blood
34	chr15:57178200-57179000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr15:57178200-57179000	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr15:57178200-57180200	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr15:57178400-57178600	Enhancers	H9 Cell Line	embryonic stem cell
38	chr15:57178400-57178600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:57178400-57178600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:57178400-57178600	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr15:57178400-57178600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr15:57178400-57178600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr15:57178400-57178600	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr15:57178400-57178600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:57178400-57178600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:57178400-57178600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:57178400-57178600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:57178400-57178600	Enhancers	Adipose Nuclei	Adipose
49	chr15:57178400-57178600	Enhancers	Liver	Liver
50	chr15:57178400-57178600	Enhancers	Brain Anterior Caudate	brain

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