Variant report

Variant	rs6715861
Chromosome Location	chr2:74432638-74432639
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	chr2:74432638-74434175	GM12878	blood:	n/a	n/a
2	ELF1	chr2:74432591-74433130	GM12878	blood:	n/a	chr2:74432876-74432889
3	ELF1	chr2:74432560-74433293	MCF-7	breast:	n/a	chr2:74432876-74432889
4	POLR2A	chr2:74432388-74433832	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:74432601-74433103	HCT-116	colon:	n/a	n/a
6	POLR2A	chr2:74432622-74434296	GM12892	blood:	n/a	n/a
7	POLR2A	chr2:74432615-74433812	GM12891	blood:	n/a	n/a
8	POLR2A	chr2:74432297-74433208	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr2:74432584-74433104	K562	blood:	n/a	n/a
10	STAT1	chr2:74432625-74433867	Hela-S3	cervix:	n/a	chr2:74433467-74433478 chr2:74433463-74433483 chr2:74433317-74433325 chr2:74433469-74433477 chr2:74433392-74433400 chr2:74433466-74433480
11	POLR2A	chr2:74432209-74432874	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr2:74432278-74433850	A549	lung:	n/a	n/a
13	POLR2A	chr2:74432633-74433030	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr2:74431026-74433991	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:74210903..74212994-chr2:74431667..74434283,2	MCF-7	breast:
2	chr2:74405932..74407579-chr2:74429494..74432993,3	MCF-7	breast:
3	chr2:74431867..74433387-chr2:74475531..74477876,2	MCF-7	breast:

Variant related genes	Relation type
MTHFD2	TF binding region
ENSG00000235499	Chromatin interaction
ENSG00000114978	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs56067994	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56370917	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57421736	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61023892	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6737355	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6749199	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73948705	0.95[AFR][1000 genomes]
rs73948708	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73952061	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73952063	1.00[EUR][1000 genomes]
rs7562660	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7598273	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
3	nsv834261	chr2:74391709-74613720	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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	81 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74427200-74433600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:74427200-74433600	Weak transcription	Lung	lung
3	chr2:74427200-74438200	Weak transcription	Fetal Kidney	kidney
4	chr2:74427400-74432800	Weak transcription	Gastric	stomach
5	chr2:74427400-74432800	Weak transcription	Right Atrium	heart
6	chr2:74427400-74432800	Weak transcription	Thymus	Thymus
7	chr2:74427400-74433400	Weak transcription	Esophagus	oesophagus
8	chr2:74427400-74435400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:74427400-74441000	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:74427400-74441200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:74427400-74448400	Weak transcription	Brain Anterior Caudate	brain
12	chr2:74427400-74453000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:74427400-74453200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:74427400-74460200	Weak transcription	Brain Substantia Nigra	brain
15	chr2:74427400-74462000	Weak transcription	Brain Angular Gyrus	brain
16	chr2:74427400-74484400	Weak transcription	Fetal Lung	lung
17	chr2:74427600-74435200	Weak transcription	Fetal Brain Female	brain
18	chr2:74427600-74435600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:74427600-74436600	Weak transcription	Right Ventricle	heart
20	chr2:74427600-74442600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:74427800-74433400	Weak transcription	NH-A	brain
22	chr2:74427800-74435000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:74427800-74494200	Weak transcription	Brain Germinal Matrix	brain
24	chr2:74428000-74435200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:74428000-74435200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:74428000-74448600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:74428600-74449600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:74428800-74432800	Weak transcription	Left Ventricle	heart
29	chr2:74428800-74433000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:74429000-74435000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:74429000-74450600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:74429000-74453200	Weak transcription	Ovary	ovary
33	chr2:74429200-74433000	Weak transcription	Stomach Mucosa	stomach
34	chr2:74429200-74433400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:74429200-74433800	Genic enhancers	Dnd41	blood
36	chr2:74429200-74452800	Weak transcription	Fetal Heart	heart
37	chr2:74429400-74433000	Weak transcription	NHLF	lung
38	chr2:74429400-74433200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:74429600-74432800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:74429600-74432800	Weak transcription	NHDF-Ad	bronchial
41	chr2:74429600-74433200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:74429600-74433600	Weak transcription	HSMMtube	muscle
43	chr2:74430200-74433200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:74430200-74433800	Genic enhancers	H1 Cell Line	embryonic stem cell
45	chr2:74430200-74433800	Genic enhancers	K562	blood
46	chr2:74430600-74433600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr2:74431200-74433800	Genic enhancers	HepG2	liver
48	chr2:74431200-74434200	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr2:74431400-74432800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:74431400-74433000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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