Variant report

Variant	rs1020396
Chromosome Location	chr2:98330826-98330827
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98330772..98333242-chr2:98334688..98336662,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1042705	0.81[CHB][hapmap]
rs10496323	1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[LWK][hapmap];0.89[ASN][1000 genomes]
rs11123849	0.81[CHB][hapmap]
rs11123861	0.80[CHB][hapmap];0.81[LWK][hapmap]
rs11547232	0.89[ASN][1000 genomes]
rs11680855	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11893601	0.81[CHB][hapmap]
rs11894651	0.81[CHB][hapmap]
rs12994966	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13000505	0.89[ASN][1000 genomes]
rs13034349	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1463173	0.80[CHB][hapmap]
rs1463174	1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[ASN][1000 genomes]
rs1800649	0.95[CHB][hapmap];0.87[CHD][hapmap];0.81[LWK][hapmap];0.91[ASN][1000 genomes]
rs1823324	0.81[CHB][hapmap]
rs2053824	0.81[CHB][hapmap]
rs2276645	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290124	0.81[CHB][hapmap]
rs35211079	0.89[ASN][1000 genomes]
rs55772322	0.88[ASN][1000 genomes]
rs56281704	0.90[ASN][1000 genomes]
rs62157580	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
2	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
3	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS 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	28 gene(s)	inside rSNPs	diseases
4	nsv874696	chr2:98309882-98362907	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv33510	chr2:98317103-98341302	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1020396	ACTR1B	cis	cerebellum	SCAN
rs1020396	ANKRD36B	cis	cerebellum	SCAN
rs1020396	ZAP70	cis	cerebellum	SCAN

Chromatin state (count:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98326200-98333000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:98329000-98331000	Enhancers	Primary hematopoietic stem cells	blood
3	chr2:98329000-98331600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:98329000-98331600	Enhancers	Fetal Muscle Trunk	muscle
5	chr2:98329000-98331800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr2:98329000-98336000	Enhancers	Fetal Muscle Leg	muscle
7	chr2:98329400-98331400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:98329400-98332000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr2:98329600-98331800	Active TSS	Colonic Mucosa	Colon
10	chr2:98329800-98331400	Active TSS	Rectal Smooth Muscle	rectum
11	chr2:98329800-98332400	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr2:98330000-98331000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
13	chr2:98330000-98331000	Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr2:98330000-98331000	Active TSS	Placenta	Placenta
15	chr2:98330000-98331200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:98330000-98331200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:98330000-98331400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:98330000-98331400	Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr2:98330000-98331400	Active TSS	Duodenum Mucosa	Duodenum
20	chr2:98330000-98331400	Active TSS	Esophagus	oesophagus
21	chr2:98330000-98331600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr2:98330000-98332400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:98330000-98337200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:98330200-98331000	Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr2:98330200-98331000	Active TSS	Small Intestine	intestine
26	chr2:98330200-98331000	Active TSS	Thymus	Thymus
27	chr2:98330200-98331200	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr2:98330200-98332000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:98330200-98332000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:98330200-98332200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
31	chr2:98330200-98334800	Weak transcription	GM12878-XiMat	blood
32	chr2:98330200-98335800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:98330400-98331200	Active TSS	Lung	lung
34	chr2:98330400-98333600	Transcr. at gene 5' and 3'	Dnd41	blood
35	chr2:98330600-98331000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr2:98330600-98331200	Enhancers	Primary B cells from cord blood	blood
37	chr2:98330600-98331400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:98330600-98331800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:98330800-98331000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr2:98330800-98331200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:98330800-98331200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:98330800-98331200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:98330800-98331200	Bivalent Enhancer	HepG2	liver
44	chr2:98330800-98331800	Enhancers	HMEC	breast
45	chr2:98330800-98331800	Enhancers	NHEK	skin
46	chr2:98330800-98332000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:98330800-98332800	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr2:98330800-98333000	Weak transcription	Spleen	Spleen
49	chr2:98330800-98334400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr2:98330800-98336000	Transcr. at gene 5' and 3'	Fetal Thymus	thymus

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