Variant report

Variant	rs13404643
Chromosome Location	chr2:38787227-38787228
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38779577..38781346-chr2:38785397..38787246,2	K562	blood:
2	chr2:38786011..38787740-chr2:38976954..38979344,3	K562	blood:
3	chr2:38783818..38787523-chr2:38967718..38971056,4	K562	blood:
4	chr2:38786392..38790076-chr2:38975715..38979796,3	MCF-7	breast:
5	chr2:38781921..38784416-chr2:38785346..38789078,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HNRPLL-4	chr2:38787215-38789656	NONHSAT070189

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10186867	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs10192837	0.84[AFR][1000 genomes]
rs10197071	0.84[AFR][1000 genomes]
rs10198949	1.00[AFR][1000 genomes]
rs10204840	0.89[AFR][1000 genomes]
rs13388732	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs13391054	1.00[YRI][hapmap]
rs13391755	0.89[AFR][1000 genomes]
rs13392719	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs13401946	1.00[YRI][hapmap]
rs13413591	0.89[AFR][1000 genomes]
rs13423067	0.89[AFR][1000 genomes]
rs13424641	0.89[AFR][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats 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	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv1796304	chr2:38766721-38790750	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38763600-38809600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:38768200-38812800	Weak transcription	Psoas Muscle	Psoas
3	chr2:38768400-38787800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:38768400-38788000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:38768400-38791600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:38769000-38793200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:38769200-38787800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:38769200-38788400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:38770000-38788600	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:38770400-38787400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:38770400-38787400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:38770400-38791000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:38770400-38794600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:38770600-38787400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:38770600-38794800	Weak transcription	NHEK	skin
16	chr2:38770800-38794400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:38771200-38787400	Weak transcription	HUVEC	blood vessel
18	chr2:38772800-38787400	Weak transcription	HepG2	liver
19	chr2:38775800-38821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:38776400-38787400	Weak transcription	Fetal Kidney	kidney
21	chr2:38776600-38787400	Weak transcription	Placenta	Placenta
22	chr2:38776600-38788000	Weak transcription	Brain Germinal Matrix	brain
23	chr2:38776600-38791000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:38776800-38787400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:38776800-38788800	Weak transcription	Fetal Brain Male	brain
26	chr2:38777000-38794600	Weak transcription	Brain Anterior Caudate	brain
27	chr2:38777000-38807200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:38777200-38794200	Weak transcription	Ovary	ovary
29	chr2:38777400-38792600	Weak transcription	Thymus	Thymus
30	chr2:38777600-38787400	Weak transcription	HMEC	breast
31	chr2:38778200-38791400	Weak transcription	Fetal Intestine Small	intestine
32	chr2:38778200-38794200	Weak transcription	Lung	lung
33	chr2:38779000-38791400	Weak transcription	Fetal Stomach	stomach
34	chr2:38779000-38818200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:38779400-38794800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:38779400-38821800	Weak transcription	Right Ventricle	heart
37	chr2:38779600-38787400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:38779600-38793600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:38779600-38807400	Weak transcription	Fetal Heart	heart
40	chr2:38779600-38812800	Weak transcription	Aorta	Aorta
41	chr2:38779800-38787400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:38779800-38800200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr2:38780000-38787400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr2:38780200-38794600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:38780200-38794800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr2:38780400-38791200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:38780400-38797200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr2:38780600-38787400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:38780600-38792600	Weak transcription	K562	blood
50	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus

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