Variant report

Variant	rs62318632
Chromosome Location	chr4:76437692-76437693
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr4:76437586-76438231	K562	blood:	n/a	n/a
2	SPI1	chr4:76437554-76438192	HL-60	blood:	n/a	n/a
3	RUNX3	chr4:76437662-76438304	GM12878	blood:	n/a	n/a
4	MAFK	chr4:76437510-76438961	K562	blood:	n/a	chr4:76438856-76438876
5	TBL1XR1	chr4:76437593-76438568	K562	blood:	n/a	n/a
6	ZNF384	chr4:76437593-76438297	K562	blood:	n/a	n/a
7	TEAD4	chr4:76437432-76438615	K562	blood:	n/a	n/a
8	EP300	chr4:76437674-76438453	K562	blood:	n/a	n/a
9	RCOR1	chr4:76437678-76438597	K562	blood:	n/a	n/a
10	GATA2	chr4:76437467-76438166	HUVEC	blood vessel:	n/a	n/a
11	FOS	chr4:76437464-76438085	HUVEC	blood vessel:	n/a	n/a
12	EP300	chr4:76437662-76438487	GM12878	blood:	n/a	n/a
13	BHLHE40	chr4:76437690-76438526	K562	blood:	n/a	n/a
14	TAL1	chr4:76437352-76438627	K562	blood:	n/a	n/a
15	POLR2A	chr4:76437369-76438564	K562	blood:	n/a	n/a
16	WRNIP1	chr4:76437588-76437994	GM12878	blood:	n/a	n/a
17	IRF1	chr4:76437593-76440142	K562	blood:	n/a	chr4:76438121-76438135 chr4:76438292-76438309
18	ARID3A	chr4:76437467-76438438	K562	blood:	n/a	n/a
19	MYC	chr4:76437554-76438540	K562	blood:	n/a	n/a
20	NR2F2	chr4:76437401-76438525	K562	blood:	n/a	n/a
21	ZMIZ1	chr4:76437595-76438597	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:76422807..76425261-chr4:76435739..76438350,2	MCF-7	breast:
2	chr4:76432863..76437584-chr4:76437624..76440912,10	MCF-7	breast:
3	chr4:76433807..76436085-chr4:76437020..76439277,2	MCF-7	breast:
4	chr4:76436258..76441363-chr4:76597157..76599917,7	K562	blood:
5	chr4:76229171..76231861-chr4:76436993..76438920,2	MCF-7	breast:
6	chr4:76435978..76441393-chr4:76648372..76651737,6	K562	blood:
7	chr4:76437150..76439919-chr4:76648856..76651737,3	K562	blood:
8	chr4:76437052..76441363-chr4:76597688..76599751,3	K562	blood:

No data

Variant related genes	Relation type
RCHY1	TF binding region
THAP6	TF binding region
ENSG00000163743	Chromatin interaction
ENSG00000138757	Chromatin interaction
ENSG00000138768	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10009558	0.87[EUR][1000 genomes]
rs10018377	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10020976	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022673	0.87[EUR][1000 genomes]
rs10026125	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10518139	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103482	0.87[EUR][1000 genomes]
rs13134862	0.86[EUR][1000 genomes]
rs13137105	0.86[EUR][1000 genomes]
rs1841933	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28504656	0.81[EUR][1000 genomes]
rs28609645	0.86[EUR][1000 genomes]
rs28871288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28877578	0.86[EUR][1000 genomes]
rs34402235	0.87[EUR][1000 genomes]
rs35362134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35931543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62318629	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835573	0.87[EUR][1000 genomes]
rs6838603	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657576	0.87[EUR][1000 genomes]
rs7681108	0.88[ASN][1000 genomes]
rs7685936	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7699102	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307834	0.87[EUR][1000 genomes]
rs9998576	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594687	chr4:76154064-76502748	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv534570	chr4:76214619-76498362	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62318632	RCHY1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76406600-76438800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:76425000-76438800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:76425400-76439000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:76430800-76438200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr4:76434200-76438400	Weak transcription	Placenta	Placenta
6	chr4:76435000-76438200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:76435400-76437800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:76435600-76438800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:76435800-76439000	Weak transcription	Gastric	stomach
10	chr4:76436000-76439400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr4:76436200-76438200	Enhancers	Brain Substantia Nigra	brain
12	chr4:76436200-76438600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr4:76436200-76438600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:76436200-76439400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:76436200-76440600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:76436400-76437800	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr4:76436400-76438600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr4:76436400-76439000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr4:76436400-76439200	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr4:76436600-76437800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:76436600-76437800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:76436600-76438000	Flanking Active TSS	HSMM	muscle
23	chr4:76436600-76438200	Flanking Active TSS	NHDF-Ad	bronchial
24	chr4:76436600-76438400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr4:76436600-76438600	Enhancers	Primary B cells from peripheral blood	blood
26	chr4:76436600-76439200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr4:76436800-76438000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr4:76436800-76438000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:76436800-76438000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr4:76436800-76438000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:76436800-76438000	Flanking Active TSS	HMEC	breast
32	chr4:76436800-76438200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr4:76436800-76438200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr4:76436800-76438400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr4:76436800-76438400	Enhancers	Small Intestine	intestine
36	chr4:76436800-76438600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr4:76436800-76438600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr4:76436800-76438800	Flanking Active TSS	HUVEC	blood vessel
39	chr4:76436800-76438800	Flanking Active TSS	K562	blood
40	chr4:76436800-76439000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr4:76437000-76437800	Flanking Active TSS	Fetal Intestine Small	intestine
42	chr4:76437000-76437800	Enhancers	Pancreas	Pancrea
43	chr4:76437000-76437800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr4:76437000-76437800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr4:76437000-76438000	Flanking Active TSS	Liver	Liver
46	chr4:76437000-76438000	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr4:76437000-76438000	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr4:76437000-76438000	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr4:76437000-76438000	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr4:76437000-76438000	Enhancers	Ovary	ovary

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