Variant report

Variant	rs2295651
Chromosome Location	chr6:24403377-24403378
allele	C/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	YY1	chr6:24403062-24403446	K562	blood:	n/a	n/a
2	MAX	chr6:24402713-24404074	HepG2	liver:	n/a	n/a
3	REST	chr6:24402834-24403795	HepG2	liver:	n/a	chr6:24403613-24403626
4	RCOR1	chr6:24402864-24403974	K562	blood:	n/a	n/a
5	TCF7L2	chr6:24402914-24403676	Hela-S3	cervix:	n/a	n/a
6	TAF1	chr6:24402880-24403565	A549	lung:	n/a	n/a
7	POLR2A	chr6:24402935-24403769	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr6:24402881-24403691	K562	blood:	n/a	n/a
9	MAZ	chr6:24402916-24403827	K562	blood:	n/a	n/a
10	MYC	chr6:24402880-24403849	K562	blood:	n/a	n/a
11	POLR2A	chr6:24402874-24403843	Hela-S3	cervix:	n/a	n/a
12	YY1	chr6:24402955-24403381	H1-hESC	embryonic stem cell:	n/a	chr6:24403010-24403021
13	PAX5	chr6:24402979-24403557	GM12878	blood:	n/a	n/a
14	BRCA1	chr6:24403104-24403405	HepG2	liver:	n/a	n/a
15	PML	chr6:24402906-24403781	K562	blood:	n/a	n/a
16	HA-E2F1	chr6:24402846-24403826	MCF-7	breast:	n/a	chr6:24403131-24403141 chr6:24403129-24403138
17	TAF1	chr6:24403034-24403397	SK-N-SH	brain:	n/a	n/a
18	PML	chr6:24402870-24403571	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:24402927-24403690	K562	blood:	n/a	n/a
20	YY1	chr6:24402947-24403437	HCT-116	colon:	n/a	chr6:24403010-24403021
21	MAX	chr6:24402946-24403870	A549	lung:	n/a	n/a
22	POLR2A	chr6:24402955-24403425	GM12891	blood:	n/a	n/a
23	RFX5	chr6:24402813-24403848	HepG2	liver:	n/a	chr6:24403729-24403746 chr6:24403730-24403745 chr6:24403730-24403745 chr6:24403730-24403745 chr6:24403476-24403485 chr6:24403473-24403488
24	POLR2A	chr6:24403066-24403443	GM12891	blood:	n/a	n/a
25	MAFK	chr6:24403285-24403464	K562	blood:	n/a	n/a
26	MAFK	chr6:24402649-24403438	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr6:24402864-24403443	SK-N-SH	brain:	n/a	n/a
28	JUND	chr6:24402907-24403613	K562	blood:	n/a	n/a
29	MAX	chr6:24402976-24403735	GM12878	blood:	n/a	n/a
30	YY1	chr6:24402938-24403725	HepG2	liver:	n/a	chr6:24403010-24403021
31	POLR2A	chr6:24402909-24403489	U87	brain:	n/a	n/a
32	POLR2A	chr6:24402913-24403634	A549	lung:	n/a	n/a
33	CTCF	chr6:24403300-24403450	GM12866	blood:	n/a	n/a
34	TBL1XR1	chr6:24403125-24403426	GM12878	blood:	n/a	n/a
35	YY1	chr6:24403025-24403642	GM12892	blood:	n/a	n/a
36	REST	chr6:24402855-24403512	K562	blood:	n/a	n/a
37	POLR2A	chr6:24402934-24403677	A549	lung:	n/a	n/a
38	RFX5	chr6:24402643-24403772	Hela-S3	cervix:	n/a	chr6:24403729-24403746 chr6:24403730-24403745 chr6:24403730-24403745 chr6:24403730-24403745 chr6:24403476-24403485 chr6:24403473-24403488
39	CHD2	chr6:24402908-24403823	Hela-S3	cervix:	n/a	n/a
40	TAF1	chr6:24402929-24403792	H1-neurons	neurons:	n/a	n/a
41	POLR2A	chr6:24402930-24403794	GM12878	blood:	n/a	n/a
42	KAP1	chr6:24403078-24403528	U2OS	brain:	n/a	n/a
43	TAF1	chr6:24402948-24403710	Hela-S3	cervix:	n/a	n/a
44	E2F6	chr6:24402963-24403755	K562	blood:	n/a	chr6:24403131-24403141 chr6:24403129-24403138
45	CBX3	chr6:24402913-24403844	K562	blood:	n/a	n/a
46	HEY1	chr6:24402843-24403839	HepG2	liver:	n/a	chr6:24403144-24403159
47	SIN3AK20	chr6:24402997-24403925	K562	blood:	n/a	n/a
48	CEBPD	chr6:24402903-24403432	HepG2	liver:	n/a	n/a
49	GABPA	chr6:24402901-24403772	K562	blood:	n/a	chr6:24403128-24403142
50	MYC	chr6:24402997-24403395	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24402909..24405943-chr6:24492830..24496087,3	K562	blood:
2	chr6:24401784..24404907-chr6:24494976..24497958,4	MCF-7	breast:

Variant related genes	Relation type
MRS2	TF binding region
ENSG00000112294	Chromatin interaction
ENSG00000112293	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10498720	1.00[CEU][hapmap]
rs12660319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661981	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes]
rs12665371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16889286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs1772254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs3761790	1.00[CEU][hapmap]
rs41271783	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61733147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793713	0.82[EUR][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	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 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	chr6:24401800-24405400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:24402400-24406600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr6:24402600-24403400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr6:24402600-24403800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:24402600-24403800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:24402600-24404000	Active TSS	Brain Angular Gyrus	brain
7	chr6:24402600-24404000	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr6:24402600-24404000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr6:24402600-24404200	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr6:24402600-24404200	Active TSS	Brain Substantia Nigra	brain
11	chr6:24402600-24404200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr6:24402600-24404400	Active TSS	Brain Cingulate Gyrus	brain
13	chr6:24402600-24404400	Active TSS	A549	lung
14	chr6:24402600-24404600	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr6:24402600-24404600	Active TSS	Rectal Smooth Muscle	rectum
16	chr6:24402600-24404600	Active TSS	Stomach Smooth Muscle	stomach
17	chr6:24402600-24404800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:24402600-24405000	Active TSS	H1 Cell Line	embryonic stem cell
19	chr6:24402600-24405200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:24402600-24405400	Active TSS	H9 Cell Line	embryonic stem cell
21	chr6:24402600-24405600	Active TSS	GM12878-XiMat	blood
22	chr6:24402800-24403400	Active TSS	Primary B cells from cord blood	blood
23	chr6:24402800-24403600	Active TSS	Liver	Liver
24	chr6:24402800-24403800	Active TSS	Primary T cells from cord blood	blood
25	chr6:24402800-24403800	Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr6:24402800-24403800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:24402800-24403800	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr6:24402800-24403800	Active TSS	Brain Hippocampus Middle	brain
29	chr6:24402800-24403800	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr6:24402800-24404000	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr6:24402800-24404000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr6:24402800-24404000	Active TSS	Lung	lung
33	chr6:24402800-24404000	Active TSS	Hela-S3	cervix
34	chr6:24402800-24404200	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr6:24402800-24404200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:24402800-24404200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:24402800-24404200	Active TSS	HSMM	muscle
38	chr6:24402800-24404400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:24402800-24404400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:24402800-24404400	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr6:24402800-24404400	Active TSS	Fetal Intestine Small	intestine
42	chr6:24402800-24404400	Active TSS	Left Ventricle	heart
43	chr6:24402800-24404600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:24402800-24404600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:24402800-24404600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:24402800-24404600	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr6:24402800-24404600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:24402800-24404600	Active TSS	Colon Smooth Muscle	Colon
49	chr6:24402800-24404600	Active TSS	Psoas Muscle	Psoas
50	chr6:24402800-24404600	Active TSS	Right Atrium	heart

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