Variant report

Variant	rs6721624
Chromosome Location	chr2:173294454-173294455
allele	A/G
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	POLR2A	chr2:173292141-173294851	MCF10A-Er-Src	breast:	n/a	n/a
2	USF1	chr2:173294372-173294772	H1-hESC	embryonic stem cell:	n/a	chr2:173294556-173294577 chr2:173294562-173294571 chr2:173294561-173294570 chr2:173294562-173294571 chr2:173294560-173294571
3	FOS	chr2:173294188-173294586	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr2:173294108-173294618	MCF10A-Er-Src	breast:	n/a	chr2:173294314-173294325
5	USF1	chr2:173294346-173294769	H1-hESC	embryonic stem cell:	n/a	chr2:173294556-173294577 chr2:173294562-173294571 chr2:173294561-173294570 chr2:173294562-173294571 chr2:173294560-173294571
6	POLR2A	chr2:173291822-173294773	HepG2	liver:	n/a	n/a
7	STAT3	chr2:173294107-173294484	MCF10A-Er-Src	breast:	n/a	chr2:173294314-173294325
8	STAT3	chr2:173294086-173294572	MCF10A-Er-Src	breast:	n/a	chr2:173294314-173294325
9	FOS	chr2:173294364-173294564	MCF10A-Er-Src	breast:	n/a	n/a
10	USF1	chr2:173294429-173294685	HepG2	liver:	n/a	chr2:173294556-173294577 chr2:173294562-173294571 chr2:173294561-173294570 chr2:173294562-173294571 chr2:173294560-173294571
11	STAT3	chr2:173294094-173294584	MCF10A-Er-Src	breast:	n/a	chr2:173294314-173294325
12	MYC	chr2:173294188-173294755	MCF10A-Er-Src	breast:	n/a	chr2:173294307-173294315 chr2:173294562-173294571 chr2:173294561-173294572 chr2:173294561-173294572
13	POLR2A	chr2:173294433-173294809	HCT-116	colon:	n/a	n/a
14	USF1	chr2:173294447-173294704	SK-N-SH_RA	brain:	n/a	chr2:173294556-173294577 chr2:173294562-173294571 chr2:173294561-173294570 chr2:173294562-173294571 chr2:173294560-173294571
15	FOS	chr2:173294154-173294588	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr2:173292139-173294695	MCF10A-Er-Src	breast:	n/a	n/a
17	MAX	chr2:173294412-173294662	HepG2	liver:	n/a	chr2:173294562-173294571 chr2:173294561-173294572 chr2:173294561-173294572
18	USF1	chr2:173294426-173294681	HepG2	liver:	n/a	chr2:173294556-173294577 chr2:173294562-173294571 chr2:173294561-173294570 chr2:173294562-173294571 chr2:173294560-173294571
19	SIN3A	chr2:173294291-173294803	H1-hESC	embryonic stem cell:	n/a	n/a
20	BHLHE40	chr2:173294161-173294743	HepG2	liver:	n/a	chr2:173294556-173294577 chr2:173294562-173294571 chr2:173294561-173294570 chr2:173294562-173294571
21	SMC3	chr2:173294045-173294533	Hela-S3	cervix:	n/a	chr2:173294157-173294171
22	MYC	chr2:173294175-173294727	MCF10A-Er-Src	breast:	n/a	chr2:173294307-173294315 chr2:173294562-173294571 chr2:173294561-173294572 chr2:173294561-173294572
23	MXI1	chr2:173291764-173294497	IMR90	lung:	n/a	n/a
24	USF2	chr2:173294393-173294720	HepG2	liver:	n/a	chr2:173294556-173294577 chr2:173294562-173294571 chr2:173294561-173294570 chr2:173294562-173294571
25	MAX	chr2:173294389-173294667	NB4	blood:	n/a	chr2:173294562-173294571 chr2:173294561-173294572 chr2:173294561-173294572

No.	Distal block	Cell Line	Cell type
1	chr2:173218614..173220137-chr2:173294190..173296145,2	K562	blood:
2	chr2:173294248..173297165-chr2:173302746..173304421,2	MCF-7	breast:
3	chr2:173290254..173291940-chr2:173293674..173296240,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226963	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12053442	0.97[ASN][1000 genomes]
rs16860515	0.84[JPT][hapmap]
rs3108779	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs6433356	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv875414	chr2:173267081-173307756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1847874	chr2:173277361-173308318	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv583663	chr2:173287832-173307756	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv583664	chr2:173289239-173307756	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6721624	KLHL23	cis	parietal	SCAN
rs6721624	UBR3	cis	cerebellum	SCAN
rs6721624	HMGCS2	trans	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173291600-173295200	Active TSS	Rectal Smooth Muscle	rectum
2	chr2:173291800-173294600	Active TSS	Brain Substantia Nigra	brain
3	chr2:173291800-173294600	Active TSS	Gastric	stomach
4	chr2:173291800-173295200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:173292000-173294600	Active TSS	Pancreas	Pancrea
6	chr2:173292000-173294600	Active TSS	Sigmoid Colon	Sigmoid Colon
7	chr2:173292000-173294800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:173292000-173294800	Active TSS	Brain Hippocampus Middle	brain
9	chr2:173292000-173295200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr2:173292000-173295600	Active TSS	Fetal Intestine Large	intestine
11	chr2:173292000-173296600	Active TSS	Right Atrium	heart
12	chr2:173292200-173294600	Active TSS	Brain Cingulate Gyrus	brain
13	chr2:173292200-173294800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:173292200-173294800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:173292200-173295000	Active TSS	Brain Anterior Caudate	brain
16	chr2:173292200-173295200	Active TSS	Colonic Mucosa	Colon
17	chr2:173292200-173295200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
18	chr2:173292200-173295600	Active TSS	Lung	lung
19	chr2:173292200-173295800	Active TSS	HMEC	breast
20	chr2:173292200-173296000	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr2:173292200-173296000	Active TSS	Duodenum Mucosa	Duodenum
22	chr2:173292200-173296200	Active TSS	Right Ventricle	heart
23	chr2:173292600-173294800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:173292600-173294800	Active TSS	Esophagus	oesophagus
25	chr2:173292600-173295000	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr2:173292800-173295200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:173293000-173294600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:173293000-173294600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:173293000-173295000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr2:173293200-173294800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:173293200-173295600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:173293200-173295800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr2:173293400-173294600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:173293400-173294800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr2:173293400-173295000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr2:173293400-173295000	Flanking Active TSS	HUVEC	blood vessel
37	chr2:173293400-173297800	Transcr. at gene 5' and 3'	NHEK	skin
38	chr2:173293600-173294600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:173293600-173294600	Flanking Active TSS	A549	lung
40	chr2:173293600-173294600	Flanking Active TSS	NHLF	lung
41	chr2:173293600-173294800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:173293600-173294800	Flanking Active TSS	Hela-S3	cervix
43	chr2:173293600-173295000	Active TSS	Fetal Muscle Trunk	muscle
44	chr2:173293600-173295200	Active TSS	Fetal Intestine Small	intestine
45	chr2:173293600-173295200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr2:173293600-173295600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr2:173293600-173296000	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr2:173293800-173294600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:173293800-173294600	Bivalent/Poised TSS	Fetal Stomach	stomach
50	chr2:173293800-173294800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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