Variant report

Variant	rs6737398
Chromosome Location	chr2:234170397-234170398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr2:234170332-234171517	GM12878	blood:	n/a	n/a
2	NFIC	chr2:234170378-234171079	GM12878	blood:	n/a	chr2:234170491-234170508
3	BCLAF1	chr2:234170370-234170801	GM12878	blood:	n/a	n/a
4	BATF	chr2:234170374-234170828	GM12878	blood:	n/a	n/a
5	NFATC1	chr2:234170361-234170862	GM12878	blood:	n/a	n/a
6	RUNX3	chr2:234170297-234171490	GM12878	blood:	n/a	n/a
7	MTA3	chr2:234170361-234171472	GM12878	blood:	n/a	n/a
8	BCLAF1	chr2:234170370-234171272	GM12878	blood:	n/a	n/a
9	TBL1XR1	chr2:234170356-234170803	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234170184..234171726-chr2:234176231..234178736,2	K562	blood:
2	chr2:234161693..234166047-chr2:234167019..234170688,4	MCF-7	breast:
3	chr2:234158513..234163302-chr2:234165991..234171009,7	K562	blood:

Variant related genes	Relation type
ATG16L1	TF binding region
ENSG00000085978	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1045095	0.80[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap]
rs10929033	0.86[ASN][1000 genomes]
rs11685932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11894529	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs13005285	0.80[CEU][hapmap];0.91[CHB][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1596016	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1816753	0.80[EUR][1000 genomes]
rs2119504	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241876	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[MEX][hapmap];0.87[ASN][1000 genomes]
rs2241877	0.87[CHB][hapmap];0.84[CHD][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs2289475	0.80[CEU][hapmap];0.95[CHB][hapmap];0.92[ASN][1000 genomes]
rs35812841	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3749079	0.86[ASN][1000 genomes]
rs3792110	0.80[CEU][hapmap];0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs4663136	0.84[CEU][hapmap];0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs6431259	0.87[ASN][1000 genomes]
rs6431262	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs6431270	0.82[ASN][1000 genomes]
rs6431655	0.87[CHB][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6431659	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6754677	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6861	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs7563345	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7587633	0.80[CEU][hapmap];0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs930449	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6737398	SCARNA5	cis	cerebellum	SCAN
rs6737398	SCARNA5	cis	parietal	SCAN
rs6737398	ATG16L1	cis	cerebellum	SCAN
rs6737398	ECEL1P2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234161400-234170600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:234161400-234170600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:234161400-234170800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:234161800-234171800	Weak transcription	Fetal Kidney	kidney
5	chr2:234161800-234180600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:234162200-234205200	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:234162200-234205200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr2:234162400-234192000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:234162400-234196400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:234162400-234205200	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr2:234162400-234205400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:234162600-234176200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:234162600-234188600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr2:234162600-234192400	Strong transcription	Osteobl	bone
15	chr2:234162600-234205000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr2:234162600-234205200	Strong transcription	Fetal Muscle Leg	muscle
17	chr2:234162800-234194000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:234162800-234197000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:234162800-234205600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:234163000-234170800	Weak transcription	Fetal Heart	heart
21	chr2:234163000-234175600	Strong transcription	Fetal Thymus	thymus
22	chr2:234163000-234176200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:234163000-234192200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:234163000-234192200	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr2:234163200-234175600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:234163200-234177800	Strong transcription	NHEK	skin
27	chr2:234163200-234188000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr2:234163200-234188800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr2:234163200-234206000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:234163800-234188600	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr2:234163800-234189000	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr2:234164000-234175400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:234164000-234175600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:234164000-234177400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:234164200-234176800	Strong transcription	Fetal Brain Female	brain
36	chr2:234164200-234178800	Strong transcription	Fetal Lung	lung
37	chr2:234164200-234205400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:234164200-234205400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:234164400-234171400	Strong transcription	Placenta	Placenta
40	chr2:234164400-234173400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:234164400-234174600	Strong transcription	Primary T cells from cord blood	blood
42	chr2:234164400-234192000	Strong transcription	NH-A	brain
43	chr2:234164400-234196800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:234164400-234197200	Strong transcription	Adipose Nuclei	Adipose
45	chr2:234164600-234174000	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr2:234164600-234175400	Strong transcription	Primary hematopoietic stem cells	blood
47	chr2:234164600-234176000	Strong transcription	Dnd41	blood
48	chr2:234164600-234176200	Strong transcription	HUVEC	blood vessel
49	chr2:234164600-234190400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:234164600-234192000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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