Variant report

Variant	rs34197800
Chromosome Location	chr2:32389646-32389647
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:32389013-32390138	K562	blood:	n/a	n/a
2	POLR2A	chr2:32389643-32390030	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:32389104-32392168	K562	blood:	n/a	n/a
4	POLR2A	chr2:32388937-32390346	K562	blood:	n/a	n/a
5	POLR2A	chr2:32389076-32390109	K562	blood:	n/a	n/a
6	POLR2A	chr2:32389523-32390043	K562	blood:	n/a	n/a
7	POLR2A	chr2:32389361-32390139	K562	blood:	n/a	n/a
8	POLR2A	chr2:32389336-32390015	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:32389471-32390067	PBDE	blood:	n/a	n/a
10	POLR2A	chr2:32388933-32390046	HepG2	liver:	n/a	n/a
11	MXI1	chr2:32389629-32391587	IMR90	lung:	n/a	n/a
12	POLR2A	chr2:32389403-32389665	ProgFib	skin:	n/a	n/a
13	MAX	chr2:32389431-32389841	K562	blood:	n/a	n/a
14	MXI1	chr2:32389527-32392277	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr2:32389520-32392007	K562	blood:	n/a	n/a
16	HEY1	chr2:32388941-32391958	K562	blood:	n/a	chr2:32391190-32391205
17	MYC	chr2:32389476-32390091	K562	blood:	n/a	n/a
18	POLR2A	chr2:32388564-32389727	K562	blood:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:32263820..32266854-chr2:32389080..32393861,5	MCF-7	breast:
2	chr2:32388440..32390986-chr2:32579691..32583834,6	K562	blood:
3	chr2:32387435..32390295-chr2:32587080..32590116,3	K562	blood:
4	chr2:32295719..32297694-chr2:32389118..32390763,2	K562	blood:
5	chr2:32263395..32265602-chr2:32389530..32391691,2	MCF-7	breast:
6	chr2:32264868..32267001-chr2:32389298..32391324,2	K562	blood:
7	chr2:32286352..32290626-chr2:32388602..32393371,12	K562	blood:
8	chr2:32107600..32109917-chr2:32388289..32390102,3	K562	blood:
9	chr2:32389583..32392652-chr2:32503120..32506003,3	K562	blood:
10	chr2:32234641..32236375-chr2:32389314..32391737,5	MCF-7	breast:
11	chr2:32286363..32290764-chr2:32387862..32393371,13	K562	blood:
12	chr2:32388385..32389940-chr2:32579717..32581806,2	K562	blood:
13	chr2:32233185..32238105-chr2:32388775..32395245,11	K562	blood:
14	chr2:32233077..32237611-chr2:32388376..32395245,10	K562	blood:
15	chr2:32388347..32391315-chr6:27100140..27102328,2	MCF-7	breast:
16	chr2:32389277..32392458-chr2:32500839..32506003,6	K562	blood:
17	chr2:32112402..32115115-chr2:32387877..32390821,4	K562	blood:
18	chr2:32264101..32266985-chr2:32387828..32391332,6	K562	blood:

No data

Variant related genes	Relation type
SLC30A6	TF binding region
ENSG00000162959	Chromatin interaction
ENSG00000119820	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000021574	Chromatin interaction
ENSG00000115760	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000162961	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11678119	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs11691939	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12478134	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[YRI][hapmap]
rs12614686	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs12991444	0.86[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap]
rs12996943	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13006495	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13006880	0.82[EUR][1000 genomes]
rs13013695	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17011801	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[YRI][hapmap]
rs177082	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs186135	0.83[EUR][1000 genomes]
rs212682	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs212683	0.80[EUR][1000 genomes]
rs212684	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs212689	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs212690	0.85[EUR][1000 genomes]
rs212691	0.85[EUR][1000 genomes]
rs212696	0.85[EUR][1000 genomes]
rs212710	0.81[EUR][1000 genomes]
rs212736	0.93[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap]
rs212742	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs212747	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs212751	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs212754	1.00[CEU][hapmap];0.89[JPT][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs212761	0.93[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2280968	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs2294178	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2366547	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs34835885	0.81[EUR][1000 genomes]
rs35978916	0.87[EUR][1000 genomes]
rs375050	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3752916	0.82[CEU][hapmap]
rs3754835	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs3769602	0.82[CEU][hapmap]
rs3769605	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs385076	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs3851310	0.82[CEU][hapmap]
rs410469	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4530415	0.96[ASN][1000 genomes]
rs462878	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4952207	0.96[ASN][1000 genomes]
rs56322034	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6543648	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6723154	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs6756085	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs686005	0.81[EUR][1000 genomes]
rs7562653	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7572964	0.82[CEU][hapmap]
rs7574000	1.00[CEU][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs805831	0.83[EUR][1000 genomes]
rs9789593	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv873778	chr2:32297984-32409007	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34197800	SLC30A6	cis	parietal	SCAN
rs34197800	SLC30A6	cis	cerebellum	SCAN
rs34197800	NLRC4	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32331600-32390200	Weak transcription	Gastric	stomach
2	chr2:32331600-32390200	Weak transcription	Pancreas	Pancrea
3	chr2:32333000-32389800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:32342200-32389800	Weak transcription	Aorta	Aorta
5	chr2:32354600-32390200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:32355000-32389800	Weak transcription	Brain Substantia Nigra	brain
7	chr2:32355000-32390200	Weak transcription	Small Intestine	intestine
8	chr2:32355400-32389800	Weak transcription	HUVEC	blood vessel
9	chr2:32355600-32389800	Weak transcription	Spleen	Spleen
10	chr2:32357400-32389800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:32360000-32390200	Weak transcription	Ovary	ovary
12	chr2:32361000-32389800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:32363400-32389800	Weak transcription	Fetal Kidney	kidney
14	chr2:32363600-32389800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:32365000-32389800	Weak transcription	Brain Anterior Caudate	brain
16	chr2:32367200-32389800	Weak transcription	Fetal Lung	lung
17	chr2:32367800-32389800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:32370000-32389800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:32371000-32390200	Weak transcription	Left Ventricle	heart
20	chr2:32371000-32390200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:32371200-32389800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:32371800-32389800	Weak transcription	Right Ventricle	heart
23	chr2:32372200-32389800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:32373800-32390000	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:32374000-32389800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:32375600-32389800	Weak transcription	Psoas Muscle	Psoas
27	chr2:32377600-32389800	Weak transcription	Fetal Stomach	stomach
28	chr2:32378000-32390000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:32379000-32389800	Weak transcription	Fetal Intestine Small	intestine
30	chr2:32379400-32390200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:32379800-32389800	Weak transcription	Primary T cells from cord blood	blood
32	chr2:32379800-32389800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:32379800-32389800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:32379800-32390000	Weak transcription	Fetal Intestine Large	intestine
35	chr2:32380000-32389800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:32380200-32389800	Weak transcription	Adipose Nuclei	Adipose
37	chr2:32380400-32389800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:32380400-32389800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr2:32380400-32389800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr2:32380400-32389800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:32380600-32390000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr2:32380800-32389800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:32381000-32389800	Weak transcription	Liver	Liver
44	chr2:32381000-32390000	Weak transcription	Placenta	Placenta
45	chr2:32381800-32389800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr2:32381800-32390200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:32382200-32389800	Weak transcription	NHDF-Ad	bronchial
48	chr2:32382200-32390000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:32383600-32390200	Weak transcription	Fetal Thymus	thymus
50	chr2:32383800-32389800	Weak transcription	HSMM	muscle

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