Variant report

Variant	rs17348638
Chromosome Location	chr2:73312572-73312573
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	RAD21	chr2:73312550-73313336	A549	lung:	n/a	chr2:73312932-73312951 chr2:73312937-73312949 chr2:73313038-73313051 chr2:73312936-73312945
2	RCOR1	chr2:73312552-73313222	IMR90	lung:	n/a	n/a
3	CTCF	chr2:73312388-73313680	SK-N-SH	brain:	n/a	chr2:73312936-73312944 chr2:73313039-73313052 chr2:73312933-73312954 chr2:73312931-73312949 chr2:73312932-73312948
4	RAD21	chr2:73312448-73313719	SK-N-SH	brain:	n/a	chr2:73312932-73312951 chr2:73312937-73312949 chr2:73313038-73313051 chr2:73312936-73312945
5	CTCF	chr2:73311873-73313353	A549	lung:	n/a	chr2:73312936-73312944 chr2:73313039-73313052 chr2:73312933-73312954 chr2:73312931-73312949 chr2:73312932-73312948
6	RAD21	chr2:73312532-73313391	HCT-116	colon:	n/a	chr2:73312932-73312951 chr2:73312937-73312949 chr2:73313038-73313051 chr2:73312936-73312945
7	SMC3	chr2:73312373-73314464	SK-N-SH	brain:	n/a	chr2:73312933-73312947 chr2:73313348-73313358
8	CTCF	chr2:73312540-73312690	GM06990	blood:	n/a	n/a
9	RAD21	chr2:73312570-73313376	HCT-116	colon:	n/a	chr2:73312932-73312951 chr2:73312937-73312949 chr2:73313038-73313051 chr2:73312936-73312945
10	POLR2A	chr2:73312529-73312607	HepG2	liver:	n/a	n/a
11	RAD21	chr2:73312540-73313286	HepG2	liver:	n/a	chr2:73312932-73312951 chr2:73312937-73312949 chr2:73313038-73313051 chr2:73312936-73312945
12	CHD1	chr2:73312428-73313302	IMR90	lung:	n/a	n/a
13	CTCF	chr2:73312568-73313390	HCT-116	colon:	n/a	chr2:73312936-73312944 chr2:73313039-73313052 chr2:73312933-73312954 chr2:73312931-73312949 chr2:73312932-73312948
14	CTCF	chr2:73312546-73313341	HCT-116	colon:	n/a	chr2:73312936-73312944 chr2:73313039-73313052 chr2:73312933-73312954 chr2:73312931-73312949 chr2:73312932-73312948

No.	Distal block	Cell Line	Cell type
1	chr2:73312393..73313765-chr2:73404147..73405159,7	K562	blood:
2	chr2:73306420..73310594-chr2:73310994..73314109,4	K562	blood:
3	chr2:73311681..73313517-chr2:73382261..73385260,2	MCF-7	breast:
4	chr2:73312425..73313439-chr2:73383446..73384426,4	K562	blood:
5	chr2:73312380..73313354-chr2:73404137..73405275,6	MCF-7	breast:
6	chr2:73296621..73300316-chr2:73309682..73312950,4	K562	blood:
7	chr2:73312436..73313489-chr2:73390495..73391503,7	MCF-7	breast:
8	chr2:73312466..73313653-chr2:73383460..73385194,13	MCF-7	breast:
9	chr2:73312534..73313377-chr2:73324583..73325513,2	K562	blood:
10	chr2:73312477..73313394-chr2:73487144..73488040,2	MCF-7	breast:
11	chr2:73312047..73313874-chr2:73383397..73384389,21	MCF-7	breast:
12	chr2:73312487..73313446-chr2:73439161..73440373,5	K562	blood:
13	chr2:73312450..73313227-chr2:73487177..73488110,3	K562	blood:
14	chr2:73311975..73313596-chr2:73382382..73383895,2	MCF-7	breast:
15	chr2:73312133..73315047-chr2:73386146..73388493,2	K562	blood:
16	chr2:73311857..73313371-chr2:73390449..73391577,9	K562	blood:
17	chr2:73312164..73314487-chr2:73402908..73404821,2	K562	blood:

Variant related genes	Relation type
RAB11FIP5	TF binding region
ENSG00000144040	Chromatin interaction
ENSG00000135631	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs17348624	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17433172	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17504663	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17504810	1.00[ASW][hapmap];0.87[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17511570	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17570040	1.00[ASW][hapmap];0.87[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17570432	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4143146	0.86[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs55633543	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55768189	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55801301	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55854246	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55881165	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55938508	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56026282	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56088054	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56161051	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56214999	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56280862	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57522927	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57666506	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57868938	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6706065	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73943009	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73943014	0.87[EUR][1000 genomes]
rs73943015	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73943016	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73943017	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73943034	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73943035	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73943036	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73943408	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73943410	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73945731	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73945733	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73945734	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73945735	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73945740	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[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	nsv1002295	chr2:73216155-73350391	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1006801	chr2:73305056-73431711	Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73299200-73314800	Weak transcription	Small Intestine	intestine
2	chr2:73299400-73314800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:73299400-73314800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:73299400-73318200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:73299400-73318400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:73299600-73312600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:73299600-73314200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:73299600-73314600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:73299600-73314800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:73299600-73315400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr2:73299600-73316000	Weak transcription	NHDF-Ad	bronchial
12	chr2:73299600-73319400	Weak transcription	K562	blood
13	chr2:73299800-73314800	Weak transcription	Brain Substantia Nigra	brain
14	chr2:73299800-73314800	Weak transcription	HSMM	muscle
15	chr2:73300000-73319200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:73300200-73314200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:73300600-73312600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:73300600-73313000	Strong transcription	Fetal Stomach	stomach
19	chr2:73302600-73312600	Weak transcription	Colon Smooth Muscle	Colon
20	chr2:73302600-73316400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:73303000-73328600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:73303200-73320600	Weak transcription	Psoas Muscle	Psoas
23	chr2:73303400-73312600	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:73303400-73313600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:73303400-73320000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:73304400-73314200	Weak transcription	HSMMtube	muscle
27	chr2:73305600-73313400	Weak transcription	NH-A	brain
28	chr2:73306600-73314800	Weak transcription	HMEC	breast
29	chr2:73307000-73313800	Weak transcription	Left Ventricle	heart
30	chr2:73307200-73314000	Weak transcription	Brain Angular Gyrus	brain
31	chr2:73307400-73314400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr2:73307800-73313800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:73307800-73314800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:73308000-73313600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:73308000-73313800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:73308400-73312600	Weak transcription	Aorta	Aorta
37	chr2:73308400-73314400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:73308600-73312600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:73308600-73313400	Weak transcription	Right Ventricle	heart
40	chr2:73308800-73312600	Weak transcription	Brain Anterior Caudate	brain
41	chr2:73308800-73313600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:73309000-73312600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr2:73309000-73312600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr2:73309000-73314000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:73309000-73314200	Weak transcription	Esophagus	oesophagus
46	chr2:73309000-73314400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:73309200-73312600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:73309200-73312600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:73309200-73312600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr2:73309200-73314600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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