Variant report

Variant	rs1635554
Chromosome Location	chr12:48374513-48374514
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48373823..48376376-chr12:48383731..48387007,3	MCF-7	breast:
2	chr12:48246296..48248237-chr12:48373548..48375566,2	MCF-7	breast:
3	chr12:48370423..48373200-chr12:48373445..48376245,2	K562	blood:
4	chr12:48293420..48296418-chr12:48372974..48374777,2	K562	blood:
5	chr12:48372717..48377052-chr12:48391617..48394178,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11168291	1.00[CHD][hapmap]
rs1635557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17122571	1.00[MEX][hapmap]
rs1793959	0.91[CEU][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4760607	1.00[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs6580650	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv525456	chr12:48366449-48376969	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv558789	chr12:48368541-48376869	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1635554	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48358600-48381400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:48359200-48384000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:48363400-48374800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:48363400-48375000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:48363400-48375000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:48363400-48383000	Weak transcription	Spleen	Spleen
7	chr12:48364400-48381200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:48365200-48381600	Weak transcription	Right Atrium	heart
9	chr12:48365400-48381000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:48366200-48381200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:48366200-48381400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:48366200-48381600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:48366600-48375200	Weak transcription	Gastric	stomach
14	chr12:48366800-48374800	Weak transcription	HepG2	liver
15	chr12:48370400-48374800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:48372400-48378400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:48373000-48375000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:48373800-48376800	Enhancers	Fetal Intestine Large	intestine
19	chr12:48374000-48375400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr12:48374200-48377600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:48374400-48376400	Genic enhancers	Fetal Intestine Small	intestine

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