Variant report

Variant	rs6459378
Chromosome Location	chr6:14828116-14828117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:14819420..14822356-chr6:14826682..14829050,2	K562	blood:
2	chr6:14828090..14830220-chr6:14891865..14894171,2	MCF-7	breast:
3	chr6:14820856..14822740-chr6:14826682..14829114,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs233495	0.87[EUR][1000 genomes]
rs233496	0.83[ASN][1000 genomes]
rs372827	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs404238	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs411347	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs452951	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715927	0.82[ASN][1000 genomes]
rs6459379	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7755454	0.97[ASN][1000 genomes]
rs865082	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	nsv1023685	chr6:14514647-14838390	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1031668	chr6:14774036-15044308	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv538138	chr6:14774036-15044308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6459378	CA4	trans	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:14819400-14828400	Weak transcription	Colonic Mucosa	Colon
2	chr6:14824600-14828800	Enhancers	Fetal Intestine Large	intestine
3	chr6:14824600-14829200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:14825000-14828600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:14825000-14828600	Enhancers	Fetal Intestine Small	intestine
6	chr6:14825600-14830600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:14825800-14828600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:14825800-14830600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr6:14826000-14829400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr6:14826200-14828200	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr6:14826200-14832000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:14826800-14830200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:14827000-14828400	Enhancers	Fetal Kidney	kidney
14	chr6:14827200-14828200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr6:14827200-14828600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:14827400-14828600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:14827400-14831800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:14827600-14828200	Enhancers	Primary B cells from cord blood	blood
19	chr6:14827600-14829000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:14827600-14829000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr6:14827600-14829200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:14827800-14828600	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr6:14827800-14829200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:14827800-14829200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:14827800-14829200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:14827800-14829200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:14827800-14829400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:14827800-14830600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:14828000-14828800	Bivalent Enhancer	Fetal Muscle Leg	muscle
30	chr6:14828000-14829200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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