Variant report

Variant	rs7591742
Chromosome Location	chr2:55507333-55507334
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BACH1	chr2:55507233-55507574	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr2:55506288-55508158	H1-hESC	embryonic stem cell:	n/a	n/a
3	HDAC2	chr2:55507167-55507604	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr2:55506519-55507868	H1-hESC	embryonic stem cell:	n/a	n/a
5	CHD2	chr2:55507226-55507516	H1-hESC	embryonic stem cell:	n/a	n/a
6	SP1	chr2:55507111-55507358	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr2:55507276-55507544	H1-hESC	embryonic stem cell:	n/a	n/a
8	POU5F1	chr2:55507107-55507456	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55494928..55498059-chr2:55506695..55512310,8	K562	blood:
2	chr2:55491409..55498987-chr2:55507178..55511380,11	MCF-7	breast:

No data

Variant related genes	Relation type
PRORSD1P	TF binding region
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12623137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1437396	0.81[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[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	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv1799450	chr2:55494904-55520842	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7591742	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55496600-55508800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:55497000-55508800	Weak transcription	Right Atrium	heart
3	chr2:55497400-55508800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:55497600-55508800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:55501000-55517000	Weak transcription	Hela-S3	cervix
6	chr2:55504800-55508800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:55505400-55508800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:55505400-55508800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr2:55505600-55508800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:55505800-55507800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr2:55506000-55507400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:55506000-55508600	Enhancers	K562	blood
13	chr2:55506200-55507400	Enhancers	HepG2	liver
14	chr2:55506200-55507800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:55506400-55507800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:55506600-55507400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:55506600-55507400	Active TSS	H9 Cell Line	embryonic stem cell
18	chr2:55506600-55507400	Enhancers	Fetal Intestine Large	intestine
19	chr2:55506600-55507800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr2:55506600-55507800	Enhancers	Fetal Intestine Small	intestine
21	chr2:55506600-55508000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:55506600-55508600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:55506600-55508800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:55506800-55507800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:55506800-55507800	Weak transcription	HMEC	breast
26	chr2:55506800-55508800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:55506800-55508800	Weak transcription	Pancreas	Pancrea
28	chr2:55507000-55508800	Weak transcription	Brain Germinal Matrix	brain
29	chr2:55507200-55507400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:55507200-55507600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr2:55507200-55507800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr2:55507200-55507800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr2:55507200-55507800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr2:55507200-55507800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr2:55507200-55507800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:55507200-55508000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr2:55507200-55508000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr2:55507200-55508600	Enhancers	NHEK	skin

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