Variant report

Variant	rs9459644
Chromosome Location	chr6:166722701-166722702
allele	A/G
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	MAX	chr6:166722673-166723223	H1-hESC	embryonic stem cell:	n/a	n/a
2	GATA3	chr6:166722349-166723173	MCF-7	breast:	n/a	n/a
3	E2F6	chr6:166722674-166723333	H1-hESC	embryonic stem cell:	n/a	n/a
4	HDAC2	chr6:166722510-166723093	MCF-7	breast:	n/a	n/a
5	GATA3	chr6:166722568-166722804	SH-SY5Y	brain:	n/a	n/a
6	TCF7L2	chr6:166722565-166722852	MCF-7	breast:	n/a	n/a
7	GATA3	chr6:166722559-166722874	T-47D	breast:	n/a	n/a
8	NR2F2	chr6:166722492-166723108	MCF-7	breast:	n/a	n/a
9	SIN3AK20	chr6:166722521-166723173	MCF-7	breast:	n/a	n/a
10	GATA3	chr6:166722618-166722972	MCF-7	breast:	n/a	n/a
11	FOXA2	chr6:166722653-166722981	HepG2	liver:	n/a	n/a
12	MAX	chr6:166722553-166723165	MCF-7	breast:	n/a	n/a
13	FOXA1	chr6:166722598-166723067	HepG2	liver:	n/a	chr6:166722826-166722841 chr6:166722805-166722820
14	FOXA1	chr6:166722620-166722986	T-47D	breast:	n/a	chr6:166722826-166722841 chr6:166722805-166722820
15	GATA3	chr6:166722265-166722979	MCF-7	breast:	n/a	n/a
16	FOXA1	chr6:166722587-166723099	HepG2	liver:	n/a	chr6:166722826-166722841 chr6:166722805-166722820
17	FOXA1	chr6:166722614-166723105	HepG2	liver:	n/a	chr6:166722826-166722841 chr6:166722805-166722820
18	FOXA1	chr6:166722606-166722977	T-47D	breast:	n/a	chr6:166722826-166722841 chr6:166722805-166722820
19	GATA3	chr6:166722493-166722927	T-47D	breast:	n/a	n/a
20	POLR2A	chr6:166721640-166722837	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:166722651..166724604-chr6:166784233..166785851,2	K562	blood:
2	chr6:166722484..166724020-chr6:166795532..166798475,2	K562	blood:
3	chr6:166722635..166726585-chr6:166755013..166756920,3	K562	blood:
4	chr6:166722256..166724406-chr6:166752301..166754007,2	MCF-7	breast:

Variant related genes	Relation type
PRR18	TF binding region
ENSG00000060762	Chromatin interaction
ENSG00000198818	Chromatin interaction
ENSG00000261420	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10946154	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10946155	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10946156	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12524268	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12526794	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12662920	0.88[ASN][1000 genomes]
rs13218257	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1575145	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4710040	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913024	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6913025	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6935260	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6935275	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9457164	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9459648	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9459649	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9459650	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9459651	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886934	chr6:166642850-166747572	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv886935	chr6:166704744-166726566	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv886936	chr6:166714024-166731289	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv3421182	chr6:166720387-166722935	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9459644	CASD1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166720600-166723000	Flanking Active TSS	Liver	Liver
2	chr6:166722000-166723000	Enhancers	Gastric	stomach
3	chr6:166722200-166722800	Weak transcription	Right Atrium	heart
4	chr6:166722200-166723000	Flanking Bivalent TSS/Enh	HepG2	liver
5	chr6:166722400-166722800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
6	chr6:166722400-166722800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
7	chr6:166722400-166722800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
8	chr6:166722400-166723000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
9	chr6:166722400-166723000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:166722400-166723000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:166722400-166723000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
12	chr6:166722400-166723000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:166722400-166723000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:166722400-166723000	Flanking Active TSS	Brain Substantia Nigra	brain
15	chr6:166722400-166723000	Bivalent Enhancer	Stomach Mucosa	stomach
16	chr6:166722400-166723200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:166722400-166723200	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr6:166722400-166723200	Bivalent Enhancer	Fetal Intestine Large	intestine
19	chr6:166722400-166723400	Bivalent Enhancer	Fetal Intestine Small	intestine
20	chr6:166722400-166723800	Enhancers	Brain Cingulate Gyrus	brain
21	chr6:166722600-166722800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
22	chr6:166722600-166722800	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr6:166722600-166723200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
24	chr6:166722600-166723200	Enhancers	Brain Hippocampus Middle	brain
25	chr6:166722600-166723200	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr6:166722600-166732800	Weak transcription	GM12878-XiMat	blood
27	chr6:166722600-166735600	Weak transcription	Brain Angular Gyrus	brain

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