Variant report

Variant	rs1035138
Chromosome Location	chr2:39999341-39999342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr2:39999252-39999546	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr2:39999336-39999488	H1-hESC	embryonic stem cell:	n/a	n/a
3	STAT3	chr2:39998999-39999406	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr2:39999156-39999497	MCF10A-Er-Src	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:39999331-39999381	HL-60	blood:	n/a
2	chr2:39999331-39999381	HRPEpiC	eye:	n/a
3	chr2:39999331-39999381	HEEpiC	esophagus:	n/a
4	chr2:39999331-39999381	IMR90	lung:	fetal
5	chr2:39999331-39999381	SK-N-MC	brain:	n/a
6	chr2:39999331-39999381	RPTEC	kidney:	n/a
7	chr2:39999331-39999381	NT2-D1	testis:	n/a
8	chr2:39999331-39999381	AG09319	gingival:	n/a
9	chr2:39999331-39999381	SKMC	muscle:	n/a
10	chr2:39999331-39999381	AG09309	skin:	n/a
11	chr2:39999331-39999381	T-47D	breast:	n/a
12	chr2:39999331-39999381	ProgFib	skin:	n/a
13	chr2:39999331-39999381	GM19239	blood:	n/a
14	chr2:39999331-39999381	GM06990	blood:	n/a
15	chr2:39999331-39999381	HepG2	liver:	n/a
16	chr2:39999331-39999381	Jurkat	blood:	n/a
17	chr2:39999331-39999381	NH-A	brain:	n/a
18	chr2:39999331-39999381	ovcar-3	ovarian:	n/a
19	chr2:39999331-39999381	Hepatocyte	liver:	n/a
20	chr2:39999331-39999381	MCF10A-Er-Src	breast:	n/a
21	chr2:39999331-39999381	Caco-2	colon:	n/a
22	chr2:39999331-39999381	K562	blood:	n/a
23	chr2:39999331-39999381	HIPEpiC	eye:	n/a
24	chr2:39999331-39999381	AG04449	skin:	fetal
25	chr2:39999331-39999381	PANC-1	pancreas:	n/a
26	chr2:39999331-39999381	HCT-116	colon:	n/a
27	chr2:39999331-39999381	LNCaP	prostate:	n/a
28	chr2:39999331-39999381	HNPCEpiC	eye:	n/a
29	chr2:39999331-39999381	AoSMC	blood vessel:	n/a
30	chr2:39999331-39999381	AG10803	skin:	n/a
31	chr2:39999331-39999381	HCPEpiC	choroid plexus:	n/a
32	chr2:39999331-39999381	GM12878	blood:	n/a
33	chr2:39999331-39999381	HMEC	breast:	n/a
34	chr2:39999331-39999381	SK-N-SH	brain:	n/a
35	chr2:39999331-39999381	NB4	blood:	n/a
36	chr2:39999331-39999381	HCM	heart:	n/a
37	chr2:39999331-39999381	BE2_C	brain:	n/a
38	chr2:39999331-39999381	HUVEC	blood vessel:	n/a
39	chr2:39999331-39999381	HRE	kidney:	n/a
40	chr2:39999331-39999381	HAEpiC	amniotic membrane:	n/a
41	chr2:39999331-39999381	BJ	skin:	n/a
42	chr2:39999331-39999381	U87	brain:	n/a
43	chr2:39999331-39999381	NHDF-neo	bronchial:	n/a
44	chr2:39999331-39999381	MCF-7	breast:	n/a
45	chr2:39999331-39999381	A549	lung:	n/a
46	chr2:39999331-39999381	PFSK-1	brain:	n/a
47	chr2:39999331-39999381	ECC-1	luminal epithelium:	n/a
48	chr2:39999331-39999381	NHBE	bronchial:	n/a
49	chr2:39999331-39999381	GM12891	blood:	n/a
50	chr2:39999331-39999381	GM12892	blood:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:39997806..40003955-chr2:40003961..40007756,6	MCF-7	breast:
2	chr2:39981401..39983374-chr2:39998682..40001306,2	K562	blood:
3	chr2:39541547..39543631-chr2:39997665..39999926,2	K562	blood:
4	chr2:39999247..40000027-chr6:14903249..14904079,2	MCF-7	breast:

No data

Variant related genes	Relation type
THUMPD2	TF binding region
THUMPD2	CpG island
ENSG00000138050	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10164984	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10169390	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10174709	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10206408	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10207589	0.83[EUR][1000 genomes]
rs10211306	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1035139	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124691	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11124692	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11124693	0.87[EUR][1000 genomes]
rs12470473	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12617624	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12620957	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12623462	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12623545	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12624217	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712653	0.84[ASN][1000 genomes]
rs12712656	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13026313	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13400213	0.91[EUR][1000 genomes]
rs13425906	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13428837	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1548877	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17478972	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1986876	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2041735	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2058620	0.81[ASN][1000 genomes]
rs2110656	0.83[ASN][1000 genomes]
rs2192685	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2373689	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2540226	0.81[ASN][1000 genomes]
rs2540227	0.82[ASN][1000 genomes]
rs2716730	0.80[EUR][1000 genomes]
rs35761077	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732121	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3732122	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4670955	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4670956	0.83[ASN][1000 genomes]
rs4670957	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4670958	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4670959	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59756273	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6544242	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6719179	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6731026	0.85[ASN][1000 genomes]
rs6731450	0.86[ASN][1000 genomes]
rs6747842	0.86[ASN][1000 genomes]
rs6750252	0.86[ASN][1000 genomes]
rs6758453	0.86[ASN][1000 genomes]
rs727376	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560642	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7581406	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7590912	0.80[EUR][1000 genomes]
rs7591347	0.80[EUR][1000 genomes]
rs8265	0.81[EUR][1000 genomes]
rs917960	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs917963	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9309042	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs962262	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs997976	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv2696	chr2:39988381-40033288	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39969800-39999800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:39971000-39999800	Weak transcription	Right Ventricle	heart
5	chr2:39975000-39999800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:39978600-40000000	Weak transcription	Fetal Heart	heart
7	chr2:39984800-39999600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:39985000-40005000	Weak transcription	Colonic Mucosa	Colon
9	chr2:39985200-39999600	Weak transcription	Brain Germinal Matrix	brain
10	chr2:39985200-39999600	Weak transcription	Psoas Muscle	Psoas
11	chr2:39985200-39999800	Weak transcription	Brain Substantia Nigra	brain
12	chr2:39985200-40005000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:39985400-40005200	Weak transcription	Fetal Brain Male	brain
14	chr2:39985600-40001000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:39985800-39999400	Weak transcription	Aorta	Aorta
16	chr2:39985800-39999600	Weak transcription	Brain Angular Gyrus	brain
17	chr2:39985800-39999800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:39985800-39999800	Weak transcription	Small Intestine	intestine
19	chr2:39985800-40004800	Weak transcription	Fetal Brain Female	brain
20	chr2:39985800-40005000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:39985800-40005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:39985800-40005400	Weak transcription	Lung	lung
23	chr2:39986000-40004200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:39986200-40004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:39986800-39999400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:39987400-39999400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:39987400-39999400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:39987400-39999800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:39987400-39999800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr2:39987400-40001000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:39987400-40001000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:39987600-40001000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr2:39987600-40003200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:39988000-39999600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:39988000-40004400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:39988200-39999600	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:39991200-40000200	Strong transcription	A549	lung
38	chr2:39992000-39999400	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:39992000-40004400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:39992000-40004600	Weak transcription	Fetal Kidney	kidney
41	chr2:39995400-40000000	Strong transcription	Primary B cells from cord blood	blood
42	chr2:39995400-40000200	Strong transcription	Fetal Thymus	thymus
43	chr2:39995800-39999800	Strong transcription	Dnd41	blood
44	chr2:39996200-39999600	Weak transcription	Brain Anterior Caudate	brain
45	chr2:39996400-39999400	Weak transcription	Ovary	ovary
46	chr2:39996400-39999400	Weak transcription	NHDF-Ad	bronchial
47	chr2:39996400-39999600	Weak transcription	Adipose Nuclei	Adipose
48	chr2:39996400-39999800	Weak transcription	Gastric	stomach
49	chr2:39996400-40001000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr2:39996400-40004200	Weak transcription	Stomach Smooth Muscle	stomach

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