Variant report

Variant	rs6544972
Chromosome Location	chr2:47454527-47454528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47401787..47404343-chr2:47454142..47456763,3	MCF-7	breast:
2	chr2:47399756..47406251-chr2:47447036..47455846,12	MCF-7	breast:
3	chr2:47399705..47406684-chr2:47448496..47456698,16	K562	blood:
4	chr2:47451335..47453658-chr2:47453697..47456326,2	MCF-7	breast:
5	chr2:47399705..47405092-chr2:47450546..47458227,19	K562	blood:
6	chr2:47452345..47454121-chr2:47454262..47455774,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226087	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10169873	0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1039162	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11899830	0.95[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11899833	0.95[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12612040	0.95[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13391158	0.95[CEU][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13422681	0.85[ASW][hapmap];0.90[GIH][hapmap];0.88[MKK][hapmap]
rs17485833	1.00[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1874668	0.81[AMR][1000 genomes]
rs2132924	0.82[AMR][1000 genomes]
rs35911616	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4952877	0.95[CEU][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4953479	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7586186	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs904166	0.95[CEU][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs904167	0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	esv10649	chr2:47429316-47472670	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6544972	C2orf61	cis	cerebellum	SCAN
rs6544972	SRBD1	cis	parietal	SCAN
rs6544972	CALM2	cis	parietal	SCAN
rs6544972	TTC7A	cis	cerebellum	SCAN
rs6544972	EPCAM	cis	cerebellum	SCAN
rs6544972	THADA	cis	cerebellum	SCAN
rs6544972	CALM2	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47447200-47455400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:47447600-47455000	Enhancers	NHLF	lung
3	chr2:47448000-47455400	Enhancers	Fetal Muscle Leg	muscle
4	chr2:47450000-47455600	Enhancers	Fetal Intestine Small	intestine
5	chr2:47450000-47455800	Enhancers	K562	blood
6	chr2:47450000-47456000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:47450200-47454600	Enhancers	Liver	Liver
8	chr2:47450200-47455600	Enhancers	Fetal Intestine Large	intestine
9	chr2:47451000-47455600	Enhancers	Placenta	Placenta
10	chr2:47451600-47454600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:47452200-47455400	Enhancers	Brain Hippocampus Middle	brain
12	chr2:47452200-47455800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr2:47452400-47454600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:47452400-47454800	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr2:47452400-47455200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:47452400-47455400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr2:47452600-47454800	Enhancers	Brain Substantia Nigra	brain
18	chr2:47452600-47455200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:47452600-47455600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:47452600-47455800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:47452800-47455400	Enhancers	Fetal Brain Male	brain
22	chr2:47453000-47455400	Enhancers	Brain Cingulate Gyrus	brain
23	chr2:47453200-47454800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:47453200-47455000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr2:47453200-47455200	Enhancers	Fetal Heart	heart
26	chr2:47453200-47455400	Enhancers	HSMMtube	muscle
27	chr2:47453200-47457600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:47453200-47457800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:47453200-47459600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:47453400-47454800	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr2:47453400-47455000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr2:47453600-47454800	Weak transcription	Right Ventricle	heart
33	chr2:47453600-47455000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:47453600-47455400	Enhancers	HSMM	muscle
35	chr2:47453600-47457400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:47453600-47457600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:47453800-47454800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:47453800-47454800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:47453800-47463600	Weak transcription	Right Atrium	heart
40	chr2:47453800-47463800	Weak transcription	Spleen	Spleen
41	chr2:47454000-47454800	Enhancers	Brain Anterior Caudate	brain
42	chr2:47454000-47455000	Weak transcription	Pancreas	Pancrea
43	chr2:47454000-47457600	Weak transcription	Adipose Nuclei	Adipose
44	chr2:47454000-47458800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:47454000-47461000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:47454200-47454600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr2:47454200-47454600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:47454200-47454600	Weak transcription	Brain Angular Gyrus	brain
49	chr2:47454200-47454600	Weak transcription	Ovary	ovary
50	chr2:47454200-47454800	Enhancers	Stomach Smooth Muscle	stomach

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