Variant report

Variant	rs12500190
Chromosome Location	chr4:8021151-8021152
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	GATA2	chr4:8021116-8021595	SH-SY5Y	brain:	n/a	n/a
2	REST	chr4:8020669-8021759	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr4:8020853-8021532	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr4:8020923-8021551	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8020577..8022876-chr4:8022955..8025277,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273267	TF binding region
ENSG00000273267	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs34477140	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv829851	chr4:7958698-8049060	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv469779	chr4:7965253-8177646	Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv482448	chr4:7965253-8177646	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	nsv829852	chr4:7991906-8151267	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878580	chr4:8012167-8045469	Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv470009	chr4:8015421-8085174	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12500190	CLNK	cis	parietal	SCAN
rs12500190	EVC	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8007800-8022000	Weak transcription	Esophagus	oesophagus
2	chr4:8010600-8052000	Weak transcription	Left Ventricle	heart
3	chr4:8012400-8039000	Weak transcription	Gastric	stomach
4	chr4:8012800-8035000	Weak transcription	Pancreas	Pancrea
5	chr4:8013000-8021400	Weak transcription	Fetal Intestine Small	intestine
6	chr4:8013000-8036600	Weak transcription	Right Ventricle	heart
7	chr4:8014800-8031400	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:8016400-8027400	Weak transcription	Aorta	Aorta
9	chr4:8016600-8021600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:8017400-8040400	Weak transcription	Right Atrium	heart
11	chr4:8018800-8027200	Weak transcription	Psoas Muscle	Psoas
12	chr4:8020000-8022200	Enhancers	Placenta Amnion	Placenta Amnion
13	chr4:8020000-8031400	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:8020400-8021200	Enhancers	Brain Hippocampus Middle	brain
15	chr4:8020800-8021200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:8020800-8021400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:8020800-8021400	Enhancers	Brain Anterior Caudate	brain
18	chr4:8020800-8024000	Strong transcription	Spleen	Spleen
19	chr4:8021000-8021200	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr4:8021000-8021200	Flanking Active TSS	Brain Substantia Nigra	brain
21	chr4:8021000-8021400	Active TSS	Brain Germinal Matrix	brain
22	chr4:8021000-8022200	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr4:8021000-8022400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:8021000-8022400	Active TSS	Brain Angular Gyrus	brain

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