Variant report

Variant	rs2241435
Chromosome Location	chr2:86360916-86360917
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:86360838-86361407	K562	blood:	n/a	n/a
2	POLR2A	chr2:86360855-86360958	K562	blood:	n/a	n/a
3	POLR2A	chr2:86360554-86361199	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:86360792-86361786	K562	blood:	n/a	n/a
5	POLR2A	chr2:86360832-86361219	K562	blood:	n/a	n/a
6	POLR2A	chr2:86360446-86363329	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:86358776..86362448-chr2:86362672..86364882,4	K562	blood:
2	chr2:86353380..86355407-chr2:86359853..86362775,2	MCF-7	breast:
3	chr2:86352907..86354994-chr2:86359460..86362087,2	K562	blood:
4	chr2:86356791..86359394-chr2:86360865..86362824,2	K562	blood:
5	chr2:86359004..86362633-chr2:86421083..86423832,3	MCF-7	breast:
6	chr12:111020697..111021557-chr2:86360717..86361563,2	NB4	blood:

No data

Variant related genes	Relation type
SNORD94	TF binding region
ENSG00000273080	Chromatin interaction
ENSG00000196850	Chromatin interaction
ENSG00000208772	Chromatin interaction
ENSG00000132305	Chromatin interaction
ENSG00000132300	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10153790	0.83[AFR][1000 genomes]
rs10168635	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10171798	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs10174095	1.00[ASW][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10175597	0.87[AFR][1000 genomes]
rs10179466	0.93[AFR][1000 genomes]
rs10193712	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs1019591	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12328075	0.92[AFR][1000 genomes]
rs12612513	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12614260	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12617717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12617962	1.00[GIH][hapmap]
rs12620810	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12621992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12622715	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs12624126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13387316	0.83[AFR][1000 genomes]
rs13393659	0.81[ASW][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs13394650	1.00[YRI][hapmap]
rs13401184	0.90[AFR][1000 genomes]
rs13402568	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs13403541	0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs13404362	0.81[AFR][1000 genomes]
rs13413723	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs13422309	0.92[AFR][1000 genomes]
rs13430553	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1424520	0.82[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs1561328	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs17026854	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17026886	0.86[AFR][1000 genomes]
rs17026975	0.96[LWK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs17027011	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17584578	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17618001	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2018608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241437	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2278084	0.90[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs2278085	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2278086	0.85[AMR][1000 genomes]
rs2278087	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2278088	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs2289237	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes]
rs2303339	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303340	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28631015	0.86[AFR][1000 genomes]
rs3731819	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3770066	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3770081	0.89[EUR][1000 genomes]
rs3770087	1.00[CEU][hapmap]
rs3770089	1.00[CEU][hapmap]
rs3770090	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs3810827	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4832024	0.83[ASN][1000 genomes]
rs56104203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57020255	0.90[AFR][1000 genomes]
rs57062037	0.96[AFR][1000 genomes]
rs57083584	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57398459	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57817729	0.99[AFR][1000 genomes]
rs59947468	0.85[AMR][1000 genomes]
rs60479377	0.85[AMR][1000 genomes]
rs60649958	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60719866	0.85[AMR][1000 genomes]
rs6547659	0.86[ASN][1000 genomes]
rs6720143	0.86[ASN][1000 genomes]
rs73947314	0.93[EUR][1000 genomes]
rs9309631	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs9789563	0.87[EUR][1000 genomes]
rs9973880	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv999956	chr2:86285944-86505453	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv1012768	chr2:86285944-86506132	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv1003207	chr2:86286314-86496732	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv1000441	chr2:86286314-86508168	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv535808	chr2:86286314-86508168	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv1004442	chr2:86286480-86506132	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv916616	chr2:86289130-86509326	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv458563	chr2:86292341-86507688	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv582370	chr2:86292341-86507688	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv1009140	chr2:86294939-86506132	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv582371	chr2:86296566-86507688	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv531381	chr2:86301091-86478346	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv1001157	chr2:86301440-86508168	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2241435	C2orf23	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86334400-86362800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:86335000-86379000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:86335000-86409000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:86335200-86366600	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr2:86335200-86380800	Strong transcription	Fetal Thymus	thymus
6	chr2:86335400-86394000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:86335400-86408800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:86335600-86366600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:86335600-86366800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:86335600-86368000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr2:86335600-86369200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:86335600-86373600	Strong transcription	K562	blood
13	chr2:86335600-86378800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:86335600-86379000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:86335600-86379000	Strong transcription	Duodenum Mucosa	Duodenum
16	chr2:86335600-86379000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr2:86335600-86394000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:86335600-86401000	Strong transcription	Placenta	Placenta
19	chr2:86335600-86407400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:86335600-86408600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:86335800-86378600	Strong transcription	Fetal Brain Female	brain
22	chr2:86336000-86365800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:86336000-86378600	Strong transcription	Brain Germinal Matrix	brain
24	chr2:86336000-86378800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:86336000-86378800	Strong transcription	Liver	Liver
26	chr2:86336000-86380800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:86336000-86401200	Strong transcription	Adipose Nuclei	Adipose
28	chr2:86336200-86366600	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr2:86336600-86363000	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr2:86336600-86369400	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr2:86336600-86378600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:86336600-86378600	Strong transcription	Fetal Muscle Leg	muscle
33	chr2:86336600-86378800	Strong transcription	Fetal Intestine Large	intestine
34	chr2:86336600-86378800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr2:86336600-86378800	Strong transcription	Rectal Smooth Muscle	rectum
36	chr2:86336600-86394200	Strong transcription	Primary T cells from cord blood	blood
37	chr2:86336800-86379200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:86336800-86407400	Strong transcription	Dnd41	blood
39	chr2:86337600-86362400	Strong transcription	Brain Cingulate Gyrus	brain
40	chr2:86337600-86365800	Strong transcription	Thymus	Thymus
41	chr2:86337600-86367800	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:86337600-86369400	Strong transcription	Spleen	Spleen
43	chr2:86337600-86378600	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:86337600-86378800	Strong transcription	Stomach Smooth Muscle	stomach
45	chr2:86339400-86379000	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr2:86340000-86365800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:86340000-86366800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr2:86340800-86368000	Strong transcription	Primary hematopoietic stem cells	blood
49	chr2:86340800-86378800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:86341200-86379400	Strong transcription	Cortex derived primary cultured neurospheres	brain

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