Variant report

Variant	rs9684650
Chromosome Location	chr4:2827205-2827206
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:2827092-2827249	GM12891	blood:	n/a	n/a
2	POLR2A	chr4:2826998-2827411	GM12892	blood:	n/a	n/a
3	MYC	chr4:2827205-2827242	MCF-7	breast:	n/a	n/a
4	POLR2A	chr4:2826826-2827528	GM12892	blood:	n/a	n/a
5	POLR2A	chr4:2826971-2827382	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr4:2827022-2827486	GM12891	blood:	n/a	n/a
7	POLR2A	chr4:2827128-2827372	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr4:2827150-2827258	Gliobla	brain:	n/a	n/a
9	POLR2A	chr4:2827091-2827324	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr4:2827033-2827418	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr4:2827002-2827497	GM12891	blood:	n/a	n/a
12	POLR2A	chr4:2827028-2827383	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:2827029-2827381	GM12878	blood:	n/a	n/a
14	POLR2A	chr4:2826390-2827515	GM12878	blood:	n/a	n/a
15	POLR2A	chr4:2827039-2827404	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:2827013-2827422	HepG2	liver:	n/a	n/a
17	POLR2A	chr4:2827150-2827288	MCF-7	breast:	n/a	n/a
18	CTCF	chr4:2827199-2827291	GM19239	blood:	n/a	n/a
19	POLR2A	chr4:2827167-2828038	HL-60	blood:	n/a	n/a
20	POLR2A	chr4:2827117-2827580	H1-neurons	neurons:	n/a	n/a
21	POLR2A	chr4:2827054-2827331	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr4:2827050-2827433	GM12891	blood:	n/a	n/a
23	POU2F2	chr4:2827066-2827428	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:2827194-2827244	GM19239	blood:	n/a
2	chr4:2827194-2827244	BE2_C	brain:	n/a
3	chr4:2827194-2827244	AG09309	skin:	n/a
4	chr4:2827194-2827244	NT2-D1	testis:	n/a
5	chr4:2827194-2827244	BJ	skin:	n/a
6	chr4:2827194-2827244	HCPEpiC	choroid plexus:	n/a
7	chr4:2827194-2827244	CMK	blood:	n/a
8	chr4:2827194-2827244	PrEC	prostate:	n/a
9	chr4:2827194-2827244	GM12892	blood:	n/a
10	chr4:2827194-2827244	HEK293	kidney:	embryo
11	chr4:2827194-2827244	HUVEC	blood vessel:	n/a
12	chr4:2827194-2827244	HRCEpiC	kidney:	n/a
13	chr4:2827194-2827244	LNCaP	prostate:	n/a
14	chr4:2827194-2827244	SK-N-SH	brain:	n/a
15	chr4:2827194-2827244	AoSMC	blood vessel:	n/a
16	chr4:2827194-2827244	HCF	heart:	n/a
17	chr4:2827194-2827244	HepG2	liver:	n/a
18	chr4:2827194-2827244	SKMC	muscle:	n/a
19	chr4:2827194-2827244	K562	blood:	n/a
20	chr4:2827194-2827244	Hepatocyte	liver:	n/a
21	chr4:2827194-2827244	MCF10A-Er-Src	breast:	n/a
22	chr4:2827194-2827244	U87	brain:	n/a
23	chr4:2827194-2827244	HCT-116	colon:	n/a
24	chr4:2827194-2827244	Caco-2	colon:	n/a
25	chr4:2827194-2827244	NHBE	bronchial:	n/a
26	chr4:2827194-2827244	HPAEpiC	pulmonary alveolar:	n/a
27	chr4:2827194-2827244	NHDF-neo	bronchial:	n/a
28	chr4:2827194-2827244	MCF-7	breast:	n/a
29	chr4:2827194-2827244	A549	lung:	n/a
30	chr4:2827194-2827244	PANC-1	pancreas:	n/a
31	chr4:2827194-2827244	HCM	heart:	n/a
32	chr4:2827194-2827244	NB4	blood:	n/a
33	chr4:2827194-2827244	IMR90	lung:	fetal
34	chr4:2827194-2827244	HEEpiC	esophagus:	n/a
35	chr4:2827194-2827244	RPTEC	kidney:	n/a
36	chr4:2827194-2827244	GM12878	blood:	n/a
37	chr4:2827194-2827244	ECC-1	luminal epithelium:	n/a
38	chr4:2827194-2827244	GM06990	blood:	n/a
39	chr4:2827194-2827244	Jurkat	blood:	n/a
40	chr4:2827194-2827244	AG04450	lung:	fetal
41	chr4:2827194-2827244	GM12891	blood:	n/a
42	chr4:2827194-2827244	HIPEpiC	eye:	n/a
43	chr4:2827194-2827244	HMEC	breast:	n/a
44	chr4:2827194-2827244	ProgFib	skin:	n/a
45	chr4:2827194-2827244	T-47D	breast:	n/a
46	chr4:2827194-2827244	NH-A	brain:	n/a
47	chr4:2827194-2827244	ovcar-3	ovarian:	n/a
48	chr4:2827194-2827244	Hela-S3	cervix:	n/a
49	chr4:2827194-2827244	AG09319	gingival:	n/a
50	chr4:2827194-2827244	PFSK-1	brain:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2794820..2799191-chr4:2824314..2827597,4	MCF-7	breast:
2	chr4:2826806..2829298-chr4:2829987..2832015,2	MCF-7	breast:
3	chr4:2822103..2824509-chr4:2824545..2827389,5	MCF-7	breast:
4	chr4:2824960..2827685-chr4:2829062..2834190,6	MCF-7	breast:
5	chr4:2824402..2830718-chr4:2842859..2847645,11	MCF-7	breast:

No data

Variant related genes	Relation type
SH3BP2	TF binding region
SH3BP2	CpG island
ENSG00000087274	Chromatin interaction
ENSG00000087266	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1623454	0.88[ASN][1000 genomes]
rs1626813	0.81[ASN][1000 genomes]
rs1709003	0.88[ASN][1000 genomes]
rs1794395	0.90[ASN][1000 genomes]
rs2239727	0.90[ASN][1000 genomes]
rs231399	0.87[ASN][1000 genomes]
rs426192	0.83[ASN][1000 genomes]
rs62637887	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878444	chr4:2689449-2861090	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv470002	chr4:2701098-2836628	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878445	chr4:2704046-2831383	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv878447	chr4:2723531-2831383	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv516797	chr4:2723531-2836628	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv878448	chr4:2723531-2846799	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
9	nsv878449	chr4:2744480-2831383	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv878450	chr4:2760222-2861090	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv878451	chr4:2785556-2856687	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv878452	chr4:2789184-2830076	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv461162	chr4:2794320-2846799	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv593436	chr4:2794320-2846799	Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats 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
17	esv3345948	chr4:2826204-2829002	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	esv3379869	chr4:2827054-2830052	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	esv3440097	chr4:2827054-2831752	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2820400-2827600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr4:2820600-2832400	Weak transcription	NHDF-Ad	bronchial
3	chr4:2820600-2839000	Weak transcription	Right Atrium	heart
4	chr4:2820600-2839200	Weak transcription	Brain Angular Gyrus	brain
5	chr4:2820600-2844600	Weak transcription	Psoas Muscle	Psoas
6	chr4:2820800-2828200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:2820800-2835200	Weak transcription	HUVEC	blood vessel
8	chr4:2820800-2835400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr4:2820800-2839600	Weak transcription	NHEK	skin
10	chr4:2821000-2844400	Weak transcription	HMEC	breast
11	chr4:2821200-2831400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:2821200-2834200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr4:2821200-2835400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:2821400-2828600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:2821400-2836200	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr4:2821400-2837800	Weak transcription	Small Intestine	intestine
17	chr4:2821600-2827400	Strong transcription	Fetal Stomach	stomach
18	chr4:2821600-2835400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr4:2821800-2828600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr4:2821800-2828600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:2821800-2835800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr4:2821800-2835800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:2821800-2838000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:2821800-2838000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:2821800-2838200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:2821800-2838600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:2821800-2838800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:2821800-2844200	Weak transcription	Hela-S3	cervix
29	chr4:2822000-2831600	Weak transcription	NH-A	brain
30	chr4:2822000-2833600	Strong transcription	Primary B cells from cord blood	blood
31	chr4:2822000-2835200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:2822000-2835600	Strong transcription	Colonic Mucosa	Colon
33	chr4:2822000-2836000	Strong transcription	Primary T cells from cord blood	blood
34	chr4:2822000-2837200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:2822000-2837600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr4:2822200-2836400	Strong transcription	Thymus	Thymus
37	chr4:2822200-2837600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr4:2822400-2828200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:2822400-2835800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:2822400-2838200	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:2822600-2827600	Strong transcription	Ovary	ovary
42	chr4:2822600-2833400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr4:2822600-2835800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr4:2822600-2835800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr4:2822600-2835800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:2822600-2836200	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr4:2822600-2836600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr4:2822600-2836600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr4:2822600-2836800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:2822600-2836800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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