Variant report

Variant	rs60131290
Chromosome Location	chr2:40001914-40001915
allele	C/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	chr2:40000847-40003564	K562	blood:	n/a	n/a
2	ZNF263	chr2:40001740-40002507	HEK293-T-REx	kidney:	n/a	n/a
3	POLR2A	chr2:40001871-40002071	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:39997806..40003955-chr2:40003961..40007756,6	MCF-7	breast:
2	chr2:39909390..39911752-chr2:39999764..40002592,2	K562	blood:
3	chr2:40001641..40002163-chr3:101263430..101263949,2	MCF-7	breast:

Variant related genes	Relation type
THUMPD2	TF binding region
ENSG00000138050	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs17024157	1.00[AMR][1000 genomes]
rs17024166	1.00[AMR][1000 genomes]
rs17024174	1.00[AMR][1000 genomes]
rs17024175	1.00[AMR][1000 genomes]
rs17024189	1.00[AMR][1000 genomes]
rs17024194	1.00[AMR][1000 genomes]
rs17024197	1.00[AMR][1000 genomes]
rs17024202	1.00[AMR][1000 genomes]
rs17024206	1.00[AMR][1000 genomes]
rs17024260	1.00[AMR][1000 genomes]
rs17024275	0.83[AFR][1000 genomes]
rs17024278	1.00[AMR][1000 genomes]
rs17024282	1.00[AMR][1000 genomes]
rs17024292	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17038962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57028848	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57317087	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57564028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58054718	1.00[AMR][1000 genomes]
rs58462460	1.00[AMR][1000 genomes]
rs72934288	1.00[AMR][1000 genomes]
rs72934295	1.00[AMR][1000 genomes]
rs72934302	1.00[AMR][1000 genomes]
rs72936018	1.00[AMR][1000 genomes]
rs72936030	1.00[AMR][1000 genomes]
rs72936031	1.00[AMR][1000 genomes]
rs72936034	1.00[AMR][1000 genomes]
rs72936037	1.00[AMR][1000 genomes]
rs72936041	1.00[AMR][1000 genomes]
rs72936044	1.00[AMR][1000 genomes]
rs72936047	1.00[AMR][1000 genomes]
rs72936048	1.00[AMR][1000 genomes]
rs72936053	1.00[AMR][1000 genomes]
rs72936058	1.00[AMR][1000 genomes]
rs72936068	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936072	1.00[AMR][1000 genomes]
rs72936073	1.00[AMR][1000 genomes]
rs72936076	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936078	1.00[AMR][1000 genomes]
rs72936079	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936085	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936089	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936091	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936095	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936096	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938105	1.00[AMR][1000 genomes]
rs72938110	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938118	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938132	0.89[AFR][1000 genomes]
rs72938134	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs990404	1.00[AMR][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	chr2:39999200-40002000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:39999400-40002600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:39999600-40002400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr2:39999600-40005200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:39999800-40004400	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr2:40000000-40004400	Weak transcription	Primary B cells from cord blood	blood
42	chr2:40000000-40004400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:40000000-40006000	Weak transcription	Spleen	Spleen
44	chr2:40000200-40002200	Weak transcription	Esophagus	oesophagus
45	chr2:40000200-40002200	Enhancers	NHEK	skin
46	chr2:40000200-40003200	Weak transcription	A549	lung
47	chr2:40000200-40003800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:40000200-40003800	Weak transcription	Small Intestine	intestine
49	chr2:40000200-40004200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr2:40000200-40004200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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