Variant report

Variant	rs10204202
Chromosome Location	chr2:47514011-47514012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47398758..47404387-chr2:47507943..47515029,11	K562	blood:
2	chr2:47499816..47503436-chr2:47513629..47516577,3	MCF-7	breast:
3	chr2:47401656..47405075-chr2:47511899..47514959,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10165172	0.93[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10165417	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10168183	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10173957	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176620	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181882	0.88[AMR][1000 genomes]
rs10189331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191879	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10201528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10204097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10204159	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206713	1.00[YRI][hapmap]
rs12328197	1.00[JPT][hapmap]
rs12329350	1.00[JPT][hapmap]
rs13383554	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13383788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13386635	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13387191	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13408016	0.90[EUR][1000 genomes]
rs13412502	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13412948	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13413278	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13414080	0.80[YRI][hapmap]
rs13422346	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13422784	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13424419	1.00[JPT][hapmap]
rs17558224	1.00[JPT][hapmap]
rs28851944	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56057658	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58176408	0.89[EUR][1000 genomes]
rs59937171	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749044	1.00[JPT][hapmap]
rs72806460	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72806465	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72806485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72806489	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73926815	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931640	1.00[JPT][hapmap]

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	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	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
4	nsv457385	chr2:47468331-47552277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv581755	chr2:47468331-47552277	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10204202	ABCG8	cis	cerebellum	SCAN
rs10204202	LOC100129726	cis	parietal	SCAN
rs10204202	MCFD2	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47499600-47514400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:47501400-47516000	Weak transcription	Stomach Mucosa	stomach
3	chr2:47502000-47517200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:47506800-47514200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:47509800-47514600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:47509800-47514800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:47510400-47514400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:47510800-47514600	Weak transcription	Brain Angular Gyrus	brain
9	chr2:47510800-47516000	Weak transcription	Fetal Intestine Small	intestine
10	chr2:47511000-47514400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:47511000-47514400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:47511400-47514400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:47511400-47515800	Weak transcription	HSMMtube	muscle
14	chr2:47511600-47518400	Weak transcription	Fetal Intestine Large	intestine
15	chr2:47512000-47522400	Weak transcription	Brain Substantia Nigra	brain
16	chr2:47512200-47522400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:47512200-47523000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:47513000-47514800	Enhancers	Placenta	Placenta
19	chr2:47514000-47514400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:47514000-47514400	Enhancers	A549	lung
21	chr2:47514000-47515000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:47514000-47515400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:47514000-47515400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:47514000-47515600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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