Variant report

Variant	rs6544243
Chromosome Location	chr2:40003181-40003182
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39997806..40003955-chr2:40003961..40007756,6	MCF-7	breast:
2	chr2:40002526..40004161-chr2:40026691..40028627,2	K562	blood:

Variant related genes	Relation type
ENSG00000138050	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10177342	0.86[AFR][1000 genomes]
rs10197101	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs12712654	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs12712655	0.87[AFR][1000 genomes]
rs13393172	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs13412186	0.89[AFR][1000 genomes]
rs28406334	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57728145	0.90[AFR][1000 genomes]
rs59146573	0.88[AFR][1000 genomes]
rs61706206	0.83[AFR][1000 genomes]
rs6725034	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs6742533	0.89[YRI][hapmap]
rs6744797	0.94[AFR][1000 genomes]
rs6749057	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs6761738	0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs7564579	0.89[YRI][hapmap];0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv2696	chr2:39988381-40033288	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39985000-40005000	Weak transcription	Colonic Mucosa	Colon
4	chr2:39985200-40005000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:39985400-40005200	Weak transcription	Fetal Brain Male	brain
6	chr2:39985800-40004800	Weak transcription	Fetal Brain Female	brain
7	chr2:39985800-40005000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:39985800-40005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:39985800-40005400	Weak transcription	Lung	lung
10	chr2:39986000-40004200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:39986200-40004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:39987600-40003200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:39988000-40004400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:39992000-40004400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:39992000-40004600	Weak transcription	Fetal Kidney	kidney
16	chr2:39996400-40004200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:39996400-40005000	Weak transcription	Stomach Mucosa	stomach
18	chr2:39996600-40004600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:39997000-40003400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:39997000-40003400	Weak transcription	Fetal Intestine Large	intestine
21	chr2:39997000-40004200	Weak transcription	Thymus	Thymus
22	chr2:39997000-40004400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:39997000-40004400	Weak transcription	Fetal Stomach	stomach
24	chr2:39997000-40004400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:39997000-40004800	Weak transcription	Fetal Intestine Small	intestine
26	chr2:39997000-40005200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr2:39997000-40005400	Weak transcription	Placenta	Placenta
28	chr2:39997000-40005800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:39997200-40004200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:39997600-40003800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr2:39998600-40004400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:39998600-40004400	Weak transcription	Liver	Liver
33	chr2:39998800-40004000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr2:39999000-40004400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:39999000-40005400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:39999600-40005200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:39999800-40004400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:40000000-40004400	Weak transcription	Primary B cells from cord blood	blood
39	chr2:40000000-40004400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:40000000-40006000	Weak transcription	Spleen	Spleen
41	chr2:40000200-40003200	Weak transcription	A549	lung
42	chr2:40000200-40003800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:40000200-40003800	Weak transcription	Small Intestine	intestine
44	chr2:40000200-40004200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr2:40000200-40004200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:40000200-40004200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:40000200-40004200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:40000200-40004200	Weak transcription	Brain Anterior Caudate	brain
49	chr2:40000200-40004200	Weak transcription	NH-A	brain
50	chr2:40000200-40004400	Weak transcription	Adipose Nuclei	Adipose

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