Variant report

Variant	rs13247976
Chromosome Location	chr7:127227938-127227939
allele	A/T
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	RCOR1	chr7:127227637-127229436	IMR90	lung:	n/a	n/a
2	MAX	chr7:127227763-127229310	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:127227872-127228778	H1-hESC	embryonic stem cell:	n/a	n/a
4	CHD2	chr7:127227920-127229264	GM12878	blood:	n/a	n/a
5	MAX	chr7:127227914-127229287	K562	blood:	n/a	n/a
6	SMARCB1	chr7:127227767-127229392	Hela-S3	cervix:	n/a	n/a
7	MAZ	chr7:127227834-127229270	K562	blood:	n/a	n/a
8	SMARCC1	chr7:127227896-127229396	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr7:127227915-127229288	U87	brain:	n/a	n/a
10	TBP	chr7:127227841-127229305	H1-hESC	embryonic stem cell:	n/a	n/a
11	E2F6	chr7:127227747-127229187	K562	blood:	n/a	chr7:127228577-127228585 chr7:127228234-127228249 chr7:127227854-127227863 chr7:127228938-127228953
12	POLR2A	chr7:127227868-127229383	PFSK-1	brain:	n/a	n/a
13	EGR1	chr7:127227845-127229463	HCT-116	colon:	n/a	n/a
14	RCOR1	chr7:127227769-127229284	K562	blood:	n/a	n/a
15	ELF1	chr7:127227921-127229484	GM12878	blood:	n/a	chr7:127228241-127228253
16	SMC3	chr7:127227447-127229528	SK-N-SH	brain:	n/a	chr7:127229017-127229027 chr7:127228184-127228194
17	CTCF	chr7:127227682-127229461	A549	lung:	n/a	chr7:127229014-127229027
18	MYC	chr7:127227931-127228711	NB4	blood:	n/a	n/a
19	CBX3	chr7:127227536-127229310	K562	blood:	n/a	n/a
20	ZKSCAN1	chr7:127227799-127228454	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr7:127227695-127229210	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr7:127227455-127229197	MCF10A-Er-Src	breast:	n/a	n/a
23	MAX	chr7:127227922-127229208	NB4	blood:	n/a	n/a
24	POLR2A	chr7:127227796-127229250	K562	blood:	n/a	n/a
25	POLR2A	chr7:127227790-127229352	PBDE	blood:	n/a	n/a
26	POLR2A	chr7:127227898-127228813	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr7:127227909-127229307	U87	brain:	n/a	n/a
28	HCFC1	chr7:127227820-127229741	Hela-S3	cervix:	n/a	n/a
29	RCOR1	chr7:127227911-127228212	K562	blood:	n/a	n/a
30	POLR2A	chr7:127227689-127229609	H1-hESC	embryonic stem cell:	n/a	n/a
31	REST	chr7:127227863-127229484	H1-neurons	neurons:	n/a	chr7:127228305-127228318 chr7:127228301-127228321
32	WRNIP1	chr7:127227921-127228136	GM12878	blood:	n/a	n/a
33	CTCF	chr7:127227820-127227970	HRE	kidney:	n/a	n/a
34	MAX	chr7:127227856-127229306	MCF-7	breast:	n/a	n/a
35	POLR2A	chr7:127227822-127229307	HepG2	liver:	n/a	n/a
36	MXI1	chr7:127227510-127229573	SK-N-SH	brain:	n/a	n/a
37	CREB1	chr7:127227811-127229372	K562	blood:	n/a	n/a
38	CTCF	chr7:127227880-127228030	SAEC	small airway:	n/a	n/a
39	POLR2A	chr7:127227778-127229296	K562	blood:	n/a	n/a
40	ZBTB7A	chr7:127227933-127228865	K562	blood:	n/a	chr7:127227982-127227993 chr7:127227983-127227994
41	BHLHE40	chr7:127227835-127229248	K562	blood:	n/a	chr7:127228183-127228199 chr7:127228182-127228198
42	RAD21	chr7:127227795-127229990	SK-N-SH	brain:	n/a	chr7:127229016-127229025 chr7:127228313-127228327
43	HCFC1	chr7:127227895-127229211	K562	blood:	n/a	n/a
44	CTCF	chr7:127227796-127229651	SK-N-SH	brain:	n/a	chr7:127229014-127229027

No.	Distal block	Cell Line	Cell type
1	chr7:127226810..127231119-chr7:127290066..127293801,4	MCF-7	breast:
2	chr7:127030656..127034603-chr7:127225190..127230310,7	MCF-7	breast:
3	chr7:127227908..127231054-chr7:127231482..127236620,11	MCF-7	breast:
4	chr7:127029421..127032644-chr7:127225849..127230043,4	K562	blood:
5	chr7:127226125..127229974-chr7:127289784..127293571,8	MCF-7	breast:
6	chr7:127223375..127232960-chr7:127286940..127295803,24	K562	blood:
7	chr7:127030702..127032822-chr7:127225677..127228410,2	K562	blood:
8	chr7:127222868..127230871-chr7:127290370..127294912,16	K562	blood:
9	chr7:127223867..127227193-chr7:127227909..127230578,5	MCF-7	breast:

Variant related genes	Relation type
ARF5	TF binding region
GCC1	TF binding region
FSCN3	TF binding region
ENSG00000179562	Chromatin interaction
ENSG00000106328	Chromatin interaction
ENSG00000197157	Chromatin interaction
ENSG00000048405	Chromatin interaction
ENSG00000240790	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10487484	0.85[ASN][1000 genomes]
rs10487494	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536698	1.00[ASN][1000 genomes]
rs12706803	0.92[ASN][1000 genomes]
rs13227138	0.85[ASN][1000 genomes]
rs13235029	0.92[ASN][1000 genomes]
rs13244426	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13309235	0.85[ASN][1000 genomes]
rs1419408	0.86[ASN][1000 genomes]
rs17660187	0.85[ASN][1000 genomes]
rs17662800	0.82[ASN][1000 genomes]
rs17730185	0.82[ASN][1000 genomes]
rs17730294	0.82[ASN][1000 genomes]
rs33973710	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34121113	0.92[ASN][1000 genomes]
rs34188289	0.82[ASN][1000 genomes]
rs34195583	0.92[ASN][1000 genomes]
rs34211107	1.00[ASN][1000 genomes]
rs34365152	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34388330	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34599926	0.96[ASN][1000 genomes]
rs34814259	0.92[ASN][1000 genomes]
rs34844752	0.82[ASN][1000 genomes]
rs34881339	0.85[ASN][1000 genomes]
rs35120956	0.82[ASN][1000 genomes]
rs35144279	0.92[ASN][1000 genomes]
rs35528098	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35640048	0.82[ASN][1000 genomes]
rs35872516	0.82[ASN][1000 genomes]
rs36046498	0.82[ASN][1000 genomes]
rs3752619	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3808111	0.82[ASN][1000 genomes]
rs58451280	0.82[ASN][1000 genomes]
rs62468943	1.00[ASN][1000 genomes]
rs62481380	0.82[ASN][1000 genomes]
rs62481384	0.82[ASN][1000 genomes]
rs62483172	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957054	0.92[ASN][1000 genomes]
rs6964793	1.00[ASN][1000 genomes]
rs746238	0.82[ASN][1000 genomes]
rs7808161	0.82[ASN][1000 genomes]
rs7811506	0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831122	chr7:127143207-127357885	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127226000-127228000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:127226000-127228000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:127226200-127228000	Weak transcription	Small Intestine	intestine
4	chr7:127226400-127228800	Weak transcription	Fetal Heart	heart
5	chr7:127227600-127228000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr7:127227600-127228000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
7	chr7:127227600-127228000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:127227600-127228000	Flanking Active TSS	Brain Cingulate Gyrus	brain
9	chr7:127227600-127228000	Flanking Active TSS	Fetal Intestine Small	intestine
10	chr7:127227600-127228000	Enhancers	Lung	lung
11	chr7:127227600-127228000	Flanking Active TSS	Rectal Smooth Muscle	rectum
12	chr7:127227600-127228000	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr7:127227600-127228000	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr7:127227600-127228000	Flanking Active TSS	HepG2	liver
15	chr7:127227600-127228200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr7:127227600-127228200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:127227600-127228200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr7:127227600-127228200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr7:127227600-127228200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr7:127227600-127228200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr7:127227600-127228200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:127227600-127228200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:127227600-127228200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:127227600-127228200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr7:127227600-127228200	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr7:127227600-127228200	Flanking Active TSS	Liver	Liver
27	chr7:127227600-127228200	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr7:127227600-127228200	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr7:127227600-127228200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr7:127227600-127228200	Flanking Active TSS	Pancreas	Pancrea
31	chr7:127227600-127228200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr7:127227600-127228200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr7:127227600-127228200	Flanking Active TSS	Dnd41	blood
34	chr7:127227600-127228200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr7:127227600-127228400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr7:127227600-127228400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:127227600-127228600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr7:127227600-127229000	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr7:127227600-127229000	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr7:127227600-127229200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:127227600-127229200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:127227600-127229200	Active TSS	Primary T cells from cord blood	blood
43	chr7:127227600-127229400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:127227800-127228000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr7:127227800-127228000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr7:127227800-127228000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
47	chr7:127227800-127228000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr7:127227800-127228000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr7:127227800-127228000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
50	chr7:127227800-127228000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell

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