Variant report

Variant	rs1196880
Chromosome Location	chr12:105485309-105485310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105485255..105487201-chr12:105499969..105501573,2	K562	blood:
2	chr12:105484191..105488176-chr12:105493160..105495554,3	MCF-7	breast:
3	chr12:105351971..105353693-chr12:105484339..105486678,2	MCF-7	breast:
4	chr12:105467422..105469473-chr12:105483302..105486142,2	K562	blood:

Variant related genes	Relation type
ENSG00000136052	Chromatin interaction
ENSG00000257999	Chromatin interaction
ENSG00000136051	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10778366	0.90[ASN][1000 genomes]
rs10861327	0.83[ASN][1000 genomes]
rs10861328	0.90[ASN][1000 genomes]
rs10861329	0.90[ASN][1000 genomes]
rs10861330	0.90[ASN][1000 genomes]
rs10861331	0.90[ASN][1000 genomes]
rs10861332	0.90[ASN][1000 genomes]
rs10861333	0.90[ASN][1000 genomes]
rs10861335	0.90[ASN][1000 genomes]
rs10861336	0.90[ASN][1000 genomes]
rs1109432	0.82[EUR][1000 genomes]
rs11112347	0.83[ASN][1000 genomes]
rs11112349	0.83[ASN][1000 genomes]
rs11112350	0.88[ASN][1000 genomes]
rs11112351	0.90[ASN][1000 genomes]
rs11112352	0.90[ASN][1000 genomes]
rs11112356	0.90[ASN][1000 genomes]
rs11612252	0.90[ASN][1000 genomes]
rs11613233	0.88[ASN][1000 genomes]
rs11613261	0.90[ASN][1000 genomes]
rs1196750	0.88[EUR][1000 genomes]
rs1196766	0.84[EUR][1000 genomes]
rs1196767	0.84[EUR][1000 genomes]
rs1196768	0.82[EUR][1000 genomes]
rs1196776	0.82[EUR][1000 genomes]
rs1196778	0.82[EUR][1000 genomes]
rs1196804	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196809	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196814	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196822	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1196835	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1196836	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1196838	0.89[EUR][1000 genomes]
rs1196854	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1196856	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196860	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1196866	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196867	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1196868	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196878	0.90[EUR][1000 genomes]
rs1196879	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196882	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196883	0.99[ASN][1000 genomes]
rs1196886	0.98[ASN][1000 genomes]
rs1201657	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12367626	0.89[ASN][1000 genomes]
rs12581638	0.90[ASN][1000 genomes]
rs17242777	0.90[ASN][1000 genomes]
rs1732377	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1732378	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1732379	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2264066	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2374451	0.87[ASN][1000 genomes]
rs2440693	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440708	0.83[EUR][1000 genomes]
rs2440717	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4144467	0.83[ASN][1000 genomes]
rs4144468	0.83[ASN][1000 genomes]
rs56118650	0.83[ASN][1000 genomes]
rs56188643	0.83[ASN][1000 genomes]
rs56369757	0.83[ASN][1000 genomes]
rs727888	0.83[EUR][1000 genomes]
rs7308195	0.90[ASN][1000 genomes]
rs7311691	0.90[ASN][1000 genomes]
rs73179949	0.90[ASN][1000 genomes]
rs7962686	0.86[ASN][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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh 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	20 gene(s)	inside rSNPs	diseases
3	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105478800-105486200	Weak transcription	Right Atrium	heart
2	chr12:105483200-105485600	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr12:105483200-105487000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:105483400-105485400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr12:105483400-105485400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr12:105483400-105485600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr12:105483600-105485600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr12:105484000-105485400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr12:105484000-105485400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:105484000-105485400	Weak transcription	K562	blood
11	chr12:105484000-105485600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:105484400-105485400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:105484400-105486600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:105484600-105485400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr12:105484800-105487000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:105485200-105486000	Enhancers	H9 Cell Line	embryonic stem cell
17	chr12:105485200-105486000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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