Variant report

Variant	rs7419838
Chromosome Location	chr2:39040845-39040846
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	chr2:38976507..38979814-chr2:39040782..39043976,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRSF7-2	chr2:39039935-39040989	refGeneNc_1388_NR_028386

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10173118	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10173240	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10176932	1.00[CHB][hapmap];0.80[CHD][hapmap]
rs10197412	0.89[CEU][hapmap]
rs10865143	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs10865144	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11124646	0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs11694383	0.94[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11889280	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465043	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12469681	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12473036	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12477252	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12712621	0.86[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12712622	0.84[ASN][1000 genomes]
rs12712626	0.83[TSI][hapmap]
rs12996194	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13011522	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13014136	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13029406	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13383541	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13411868	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13417196	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1529625	0.81[CEU][hapmap]
rs1530852	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1530853	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1979142	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1997377	0.81[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap]
rs2037875	0.89[CEU][hapmap]
rs2272445	0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs2373473	1.00[JPT][hapmap]
rs3099940	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs3099941	1.00[JPT][hapmap]
rs3099943	0.90[JPT][hapmap]
rs3099945	0.90[JPT][hapmap]
rs3099952	0.91[ASN][1000 genomes]
rs3099960	0.88[ASN][1000 genomes]
rs3099965	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3099985	0.80[EUR][1000 genomes]
rs3099987	0.80[EUR][1000 genomes]
rs3099988	0.83[ASN][1000 genomes]
rs3099989	0.83[ASN][1000 genomes]
rs3099991	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3112140	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3112159	0.80[TSI][hapmap]
rs3112198	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3112200	0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3112205	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3112209	0.90[ASN][1000 genomes]
rs3112210	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3112215	0.81[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3112216	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770681	1.00[CHB][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap]
rs4602206	0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs4630748	0.92[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs4670897	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56393601	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60012208	0.80[EUR][1000 genomes]
rs62144837	0.83[EUR][1000 genomes]
rs6544175	0.86[ASN][1000 genomes]
rs6715866	0.92[CEU][hapmap]
rs6723868	0.85[ASN][1000 genomes]
rs6728394	0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs6746818	0.92[CEU][hapmap]
rs6753251	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6756847	0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs7419616	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7588621	0.81[ASN][1000 genomes]
rs7589162	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7603676	0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7419838	SFRS7	Cis_1M	lymphoblastoid	RTeQTL
rs7419838	MORN2	cis	parietal	SCAN
rs7419838	DHX57	cis	parietal	SCAN
rs7419838	DHX57	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39006400-39045600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:39009200-39042600	Weak transcription	Fetal Kidney	kidney
4	chr2:39009200-39050000	Weak transcription	HMEC	breast
5	chr2:39009200-39052800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:39017600-39042200	Weak transcription	Small Intestine	intestine
7	chr2:39019000-39057800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:39022000-39042600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:39022000-39066800	Weak transcription	Stomach Mucosa	stomach
10	chr2:39024000-39053000	Weak transcription	Psoas Muscle	Psoas
11	chr2:39025600-39042400	Weak transcription	Hela-S3	cervix
12	chr2:39025600-39042400	Weak transcription	HSMM	muscle
13	chr2:39026600-39079800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
15	chr2:39032800-39072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:39033000-39041400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:39033000-39053000	Weak transcription	Fetal Brain Male	brain
18	chr2:39033800-39050200	Weak transcription	K562	blood
19	chr2:39034200-39041400	Weak transcription	GM12878-XiMat	blood
20	chr2:39036000-39046800	Strong transcription	Fetal Stomach	stomach
21	chr2:39036000-39054000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:39036200-39043800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:39036400-39051600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:39037000-39046000	Strong transcription	Fetal Intestine Small	intestine
25	chr2:39037000-39046800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:39037200-39055800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:39037400-39041200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:39037400-39041400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:39037400-39041400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr2:39037400-39041600	Strong transcription	Placenta	Placenta
31	chr2:39037400-39043200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr2:39037400-39046000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:39037400-39046600	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:39037400-39046600	Strong transcription	Fetal Brain Female	brain
35	chr2:39037400-39046800	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr2:39037400-39047200	Strong transcription	Primary T cells from cord blood	blood
37	chr2:39037400-39047800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:39037400-39047800	Strong transcription	Left Ventricle	heart
39	chr2:39037400-39052000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:39037400-39054000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:39037400-39054000	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr2:39037400-39054600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:39037600-39043000	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr2:39037600-39043200	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr2:39037600-39043400	Strong transcription	Primary B cells from cord blood	blood
46	chr2:39037600-39046200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:39037600-39046600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:39037600-39046600	Strong transcription	Fetal Thymus	thymus
49	chr2:39037600-39046800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:39037600-39046800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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