Variant report

Variant	rs1619202
Chromosome Location	chr1:113589144-113589145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113413526..113415499-chr1:113588812..113591393,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRIG2-2	chr1:113588674-113589674	NONHSAT005313

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1216764	0.89[AFR][1000 genomes]
rs1216765	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1216788	0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1216789	0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1216794	1.00[AMR][1000 genomes]
rs1216795	1.00[AMR][1000 genomes]
rs1216806	1.00[AMR][1000 genomes]
rs1216809	1.00[AMR][1000 genomes]
rs1216811	1.00[AMR][1000 genomes]
rs1766861	0.92[ASW][hapmap];0.94[LWK][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs1778021	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2788259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2950633	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2950637	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
10	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
12	nsv946146	chr1:113567302-113640814	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113580200-113589200	Weak transcription	Right Atrium	heart
2	chr1:113584800-113589400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:113585000-113591000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:113585400-113589200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:113585600-113599200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:113585600-113601800	Weak transcription	Fetal Stomach	stomach
7	chr1:113586000-113589200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:113586200-113589200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:113586600-113589200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:113586600-113589200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:113586600-113589200	Weak transcription	K562	blood
12	chr1:113586600-113599600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:113586800-113589200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:113586800-113589200	Weak transcription	GM12878-XiMat	blood
15	chr1:113586800-113589800	Weak transcription	Fetal Intestine Large	intestine
16	chr1:113586800-113589800	Weak transcription	Fetal Intestine Small	intestine
17	chr1:113586800-113590400	Weak transcription	HepG2	liver
18	chr1:113586800-113590600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:113587400-113589200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:113587400-113589200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:113587400-113599600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:113587600-113589400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:113587600-113590200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:113587800-113589200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:113587800-113589200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:113587800-113589200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:113587800-113590200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr1:113588000-113589200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:113588000-113589200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:113588000-113589200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:113588000-113596200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:113588400-113590800	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr1:113588800-113589200	Enhancers	Primary T cells from cord blood	blood
34	chr1:113588800-113589200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr1:113588800-113589200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:113588800-113589400	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr1:113588800-113589400	Enhancers	Fetal Thymus	thymus
38	chr1:113588800-113590000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr1:113588800-113590000	Enhancers	Primary hematopoietic stem cells	blood
40	chr1:113588800-113590200	Enhancers	Primary B cells from cord blood	blood
41	chr1:113588800-113590200	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr1:113588800-113590600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:113588800-113590800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr1:113588800-113590800	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr1:113588800-113591000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr1:113589000-113589400	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr1:113589000-113589400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:113589000-113589400	Flanking Active TSS	Dnd41	blood
49	chr1:113589000-113589800	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr1:113589000-113589800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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